Re: [galaxy-dev] galaxy server file upload problem
Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 h...@syntekabio.com wrote: Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] importing a large number of samples via a sample sheet
Hey Ryan, Sorry this fell through the cracks. A script to import large sets of files to data libraries, for example, would be really easy to implement using the Galaxy API. There are several examples in the /scripts/api folder of your distribution ( https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757ae3839f0b72c/scripts/api/?at=default). I can find an explicit example of this if you're interested. -Dannon On Thu, Nov 13, 2014 at 9:08 AM, Ryan G ngsbioinformat...@gmail.com wrote: Bumping this questionno response in over a week... Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part. My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files. I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Not Displacing History
This is usually an old cached version of the history panel interfering, or a javascript error that you'd see in the console. Can you clear browser cache, close out all Galaxy windows, and try again? If that still doesn't work, can you look in the javascript console to see if there are any errors? Dropping the database and whatnot definitely shouldn't ever be required. On Wed, Nov 5, 2014 at 3:52 PM, Jeremy Liu jeremy@yale.edu wrote: Hi Galaxy Dev, I just pulled the latest updates for galaxy-dist with hg pull -u and then migrated over the postgres database with: sh manage_db.sh -c ./universe_wsgi.ini upgrade After restarting the server, my Galaxy instance would not show the history of datasets. The history was still there, since I could see it when I clicked Saved Datasets - View - Show Structure and jobs would be executed normally. However the history toolbar was entirely missing. Is there any fix for this other than dropping the database, deleting galaxy and clean install galaxy? (then reinstall the tools that I had downloaded from the toolshed). Note: After running sh run.sh --reload, Galaxy noted that some of the tools were not moved over, so I tried running sh ./scripts/migrate_tools/0012_tools.sh and sh ./scripts/migrate_tools/0012_tools.sh install_dependencies but I was unable to locate the scripts. Thanks, Jeremy Liu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] failure to export workflows
On Mon, Oct 13, 2014 at 8:14 AM, John Chilton jmchil...@gmail.com wrote: My understanding is that it was briefly optional (and maybe just through the API) but that was a bug. I think Dannon made that fix a few months ago. Sorry for the confusion. This is correct, public usernames are required and there was a bug that was incorrectly validating empty ones. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] missing fastq groomer tool on galaxy cloudman
Hi Namit, This is an oversight and that tool should be installed by default. We'll make it so in the next Cloudman release. That said, it's really easy to install this (and other tools) on your cloud instances using the toolshed. Steps: - Make yourself an admin user (see the cloudman admin interface for an easy way to do this). - Log into your Galaxy as this admin. - Click Admin in the masthead, Search and browse tool sheds on the left side, select Galaxy main tool shed, search for fastq_groomer. - Click fastq_groomer and then pick Install to Galaxy, following the rest of the prompts. Let me know if you run into any issues with this, -Dannon On Fri, Oct 10, 2014 at 1:10 PM, NAMIT KUMAR nk...@scarletmail.rutgers.edu wrote: Hello, I am using galaxy on amazon web servers ( AMI: ami-a7dbf6ce; Name: Galaxy CloudMan 2.3). This is a setup I have used several time in the past with no issue, for suddenly since yesterday- there is *NO option of fastq groomer tool* on this ami. fastq groomer tool is still available on public server but not on aws cloudman. Anyone has any information on this? best, Namit ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] quick note of thanks
Thanks Chris, it's great to hear that Cloudman worked well for you! There actually is a way to launch an instance providing a share-a-cluster string in user data for a while, (a `share_string: stuff` entry in user data) but there is, or was -- I need to test this again, a race condition in the boot logic that would sometimes have the instance go belly up on launch. On Mon, Oct 13, 2014 at 10:02 AM, Chris Dagdigian d...@sonsorol.org wrote: Wanted to send Dannon the list a quick note of thanks. Cloudman-managed Galaxy is pretty slick. I'm using it today to run 26 individual Galaxy instances running on big c3.8xlarge AWS nodes for a training class. Each of the 26 training systems is built from a shared cluster string config which means I can stand up tested systems that also contain a hidden history that students can access and refer to if they get stuck. We wanted to give each student their own individual Galaxy sandbox to play on and Cloudman made it very easy. Faster than custom configuring a personal AMI and using Chef/devOps tricks to clone and automate the deployment. All told it took me about 1.5 days to get my head around cloudman and make all the usual mistakes regarding breaking things, screwing things up and otherwise running through the learning curve. After that it took me about 1 day to load the master cluster image up with data, history and run through all of the lab exercises. After that it was about 2 hours to share the cluster and start firing up the clones One thing that would help (and perhaps this is something that I missed in the documentation) would be the ability to pass in the shared cluster string as user-data at launch time. That would have let me fire up the training nodes with a single shell script. Instead I used a shell script to fire up the nodes but then I had to hit the cloudman URL on each node to punch in the shared-cluster URI string. Thanks again! Regards, Chris ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data uploaded with new upload tool doesn't get added to history
Just to follow up on this thread -- we resolved this over IRC. It was a proxy configuration issue with nginx's upload_config settings. Correct settings are now on the wiki, but the previous rule for: location _upload_done : set $dst /tool_runner/index; is was causing a redirect and preventing communication with the tools API, which the new upload form works. -Dannon On Thu, Oct 9, 2014 at 3:00 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hey there Using the new upload tool my data uploads but never appears in the history. All I can see in paster.log when I do an upload is: 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] POST /tool_runner/index HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b/contents HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 No errors in the javascript console, and this happens with both Chrome and Firefox (on Linux), code is latest galaxy-central. Any ideas where to debug? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data uploaded with new upload tool doesn't get added to history
D'oh. It's correct in the block right above that, but incorrect there. I'll fix it now. On Fri, Oct 10, 2014 at 9:44 AM, Nicola Soranzo sora...@crs4.it wrote: Hi Dannon, so the very last line (set $dst /galaxy/tool_runner/index;) on the wiki page https://wiki.galaxyproject.org/Admin/Config/nginxProxy is still wrong? Ciao, Nicola Il giorno ven, 10/10/2014 alle 08.50 -0400, Dannon Baker ha scritto: Just to follow up on this thread -- we resolved this over IRC. It was a proxy configuration issue with nginx's upload_config settings. Correct settings are now on the wiki, but the previous rule for: location _upload_done : set $dst /tool_runner/index; is was causing a redirect and preventing communication with the tools API, which the new upload form works. -Dannon On Thu, Oct 9, 2014 at 3:00 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hey there Using the new upload tool my data uploads but never appears in the history. All I can see in paster.log when I do an upload is: 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] POST /tool_runner/index HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b/contents HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 No errors in the javascript console, and this happens with both Chrome and Firefox (on Linux), code is latest galaxy-central. Any ideas where to debug? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data uploaded with new upload tool doesn't get added to history
(And thanks for the catch!) On Fri, Oct 10, 2014 at 9:48 AM, Dannon Baker dannon.ba...@gmail.com wrote: D'oh. It's correct in the block right above that, but incorrect there. I'll fix it now. On Fri, Oct 10, 2014 at 9:44 AM, Nicola Soranzo sora...@crs4.it wrote: Hi Dannon, so the very last line (set $dst /galaxy/tool_runner/index;) on the wiki page https://wiki.galaxyproject.org/Admin/Config/nginxProxy is still wrong? Ciao, Nicola Il giorno ven, 10/10/2014 alle 08.50 -0400, Dannon Baker ha scritto: Just to follow up on this thread -- we resolved this over IRC. It was a proxy configuration issue with nginx's upload_config settings. Correct settings are now on the wiki, but the previous rule for: location _upload_done : set $dst /tool_runner/index; is was causing a redirect and preventing communication with the tools API, which the new upload form works. -Dannon On Thu, Oct 9, 2014 at 3:00 PM, Peter van Heusden p...@sanbi.ac.za wrote: Hey there Using the new upload tool my data uploads but never appears in the history. All I can see in paster.log when I do an upload is: 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] POST /tool_runner/index HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b/contents HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] GET /api/histories/f597429621d6eb2b HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 No errors in the javascript console, and this happens with both Chrome and Firefox (on Linux), code is latest galaxy-central. Any ideas where to debug? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Anyone else having issues with cloudman cloudlaunch?
Hi Chris, How are you trying to start these clusters? And, the one you started successfully, how did you start it? -Dannon On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian d...@sonsorol.org wrote: Anyone else having issues using cloudman version of galaxy? No matter what set of AWS keys I use to try to start a new galaxy cluster I always get the vague Bad Request : Instance failure, but no specific error was detected. Please check your AWS Console. ... error on the launch screen. Nothing obvious in the AWS console. I'm using both my root AWS keys as well as IAM generated keys with full admin rights and no love. I do have one running cluster; does that need to be stopped or paused before I try to launch more? Regards, Chris ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Anyone else having issues with cloudman cloudlaunch?
Just realized you said cloudlaunch in the subject there, so I'm assuming that's what you used. For both working and non-working clusters? And this is cloudlaunch on usegalaxy.org? I can check the logs for more detailed launch failures, if so. On Fri, Oct 10, 2014 at 1:27 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Chris, How are you trying to start these clusters? And, the one you started successfully, how did you start it? -Dannon On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian d...@sonsorol.org wrote: Anyone else having issues using cloudman version of galaxy? No matter what set of AWS keys I use to try to start a new galaxy cluster I always get the vague Bad Request : Instance failure, but no specific error was detected. Please check your AWS Console. ... error on the launch screen. Nothing obvious in the AWS console. I'm using both my root AWS keys as well as IAM generated keys with full admin rights and no love. I do have one running cluster; does that need to be stopped or paused before I try to launch more? Regards, Chris ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Anyone else having issues with cloudman cloudlaunch?
The errors I'm seeing in the logs relate to virtualization required baked into the AMI for the large memory instances. This is an error on our side related to new instance types. What I'd recommend to get off the ground immediately (with reasonable memory on a node) would be to use the c3.8xlarge instance type (compute optimized 8x, 60GB memory), which will launch successfully. On Fri, Oct 10, 2014 at 1:35 PM, Chris Dagdigian d...@sonsorol.org wrote: Appreciate the fast reply! I'm at a training session where I hope to spin up 24 cloudman managed galaxy instances so each student can have a 1:1 ownership of their own cluster I used this URL to fire up my test cluster: https://usegalaxy.org/cloudlaunch ... but the test cluster is running out of RAM building bowtie2 index files so I was trying to start a new cluster based on the currently running system but started on an instance type with more memory. And today when I go back to the https://usegalaxy.org/cloudlaunch I'm getting the errors I posted If there is anything in the logs I'd appreciate it. Not sure if I'm doing anything wrong on my end. Currently launching the pure base AMI without the cloudlaunch interface to see if I get further ... Regards, Chris Dannon Baker wrote: Just realized you said cloudlaunch in the subject there, so I'm assuming that's what you used. For both working and non-working clusters? And this is cloudlaunch on usegalaxy.org http://usegalaxy.org? I can check the logs for more detailed launch failures, if so. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] SQLalchemy InvalidRequestError
Ulf, Thanks for all the information, hopefully it helps me replicate this issue so I can figure out a better fix. I can work on some better documentation for this, but there aren't any Galaxy-specific instructions that I know of. Using the basic configuration for setting up the rabbitmq server (www.rabbitmq.com) should work fine, and then you just need to fill out the 'galaxy_internal_connection' part in your galaxy.ini (formerly universe_wsgi.ini) with something like (more documentation here: http://kombu.readthedocs.org/en/latest/userguide/connections.html) : amqp_internal_connection = amqp://galaxy:galaxy@localhost:5672// And galaxy should automatically do the rest of the work for you -- configuring of the exchange/queues and such. On Wed, Oct 8, 2014 at 6:58 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Hi Dannon Yes. The database is running on a different server from the server running Galaxy. They are both VMs running Centos (6.5 on the Galaxy server, 6.2 on the database server). The postgres version is 8.4.9 and the database size is 712,161,040. I suspect that is not very large compared to some others. There are a number of other databases running on the same server, the one most frequently used is for our test Galaxy server which runs on yet a different VM. This one is much smaller (25,319,184). Both servers are on the same subnet. The problem is with our production Galaxy (of course). Are there any instructions around, how to implement a rabbitmq for my Galaxy? Thanks for looking into this. Ulf On 08/10/14 11:26, Dannon Baker wrote: Hi again Ulf, Thanks for the info. A few questions to help me track this down: Does the postgres database reside on a remote box from galaxy? And is it very large? Running the latest galaxy may not change anything related to this particular issue, but you could always try it. Sqlalchemy is fixed at the latest version we can currently support without reworking how migration scripts function (which we will do, moving to Alembic, in the future), and I do suspect that this is actually a bug in sqlalchemy mapper initialization, but we should be able to come up with an interim work around. Finally, if this is a blocker for you while it's not trivial(and I still am going to fox this bug), setting up an amqp (rabbitmq) server and configuring your galaxy instances to communicate using that is a workaround. On Oct 8, 2014 10:45 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Hi all again Seems I am not so fortunate that this would just go away. It appear to be happening sometimes at start-up time for one of the handler processes. The first thing that appears to go wrong is this just after starting the job handler queue: --- galaxy.jobs.handler INFO 2014-10-06 14:37:51,220 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2014-10-06 14:37:51,246 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2014-10-06 14:37:51,253 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.queue_worker INFO 2014-10-06 14:37:51,254 Initalizing Galaxy Queue Worker on sqlalchemy+postgres://galaxy:xxx@158.119.147.86:5432/galaxyprod galaxy.jobs DEBUG 2014-10-06 14:37:51,416 (78355) Working directory for job is: /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/database/job_working_directory/078/78355 galaxy.web.framework.base DEBUG 2014-10-06 14:37:51,454 Enabling 'data_admin' controller, class: DataAdmin galaxy.jobs.handler ERROR 2014-10-06 14:37:51,464 failure running job 78355 Traceback (most recent call last): File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py, line 243, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py, line 333, in __check_if_ready_to_run state = self.__check_user_jobs( job, self.job_wrappers[job.id] ) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py, line 417, in __check_user_jobs if job.user: File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py, line 168, in __get__ return self.impl.get(instance_state(instance),dict_) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py, line 453, in get value = self.callable_(state, passive) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py, line 508, in _load_for_state return self._emit_lazyload(session, state, ident_key) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs
Re: [galaxy-dev] SQLalchemy InvalidRequestError
mapperlib.configure_mappers() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py, line 2263, in configure_mappers mapper._post_configure_properties() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py, line 1172, in _post_configure_properties prop.init() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/interfaces.py, line 128, in init self.do_init() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/properties.py, line 910, in do_init self._process_dependent_arguments() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/properties.py, line 998, in _process_dependent_arguments self.target = self.mapper.mapped_table File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/util/langhelpers.py, line 494, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/properties.py, line 891, in mapper mapper_ = mapper.class_mapper(self.argument(), File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/declarative.py, line 1428, in return_cls (prop.parent, arg, n.args[0], cls) InvalidRequestError: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name (name 'Message' is not defined). If this is a class name, consider adding this relationship() to the class 'kombu.transport.sqlalchemy.Queue' class after both dependent classes have been defined. --- After that it starts throwing the exception in monitor_step that I previously posted. Has anyone seen a potentially related issue? Would an update to the latest galaxy code help? I see there are newer versions of SQLAlchemy available. Are they part of a newer code base? Thanks a lot for your help Ulf On 07/10/14 12:20, Ulf Schaefer wrote: Update: The usual switching it off and on again (server reboot) has resolved the problem (for now), albeit in a rather unsatisfactory manner. If there are any insights what caused this behaviour and how it can be avoided in the future I'd be more than happy to hear them. Cheers Ulf On 07/10/14 11:04, Dannon Baker wrote: One per second? Can you tell me more about your configuration? This is an odd bug with multiple mapper initialization that I haven't been able to reproduce yet, so any information will help. Database configuration, number of processes, etc. On Oct 7, 2014 11:46 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear all Maybe one of you can shed some light on this error message that I see in the log file for one of my handler processes. I get about one of them per second. The effect is that most of the jobs remain in the waiting to run stage. The postgres database is running on a separate server and appear to be doing just fine. Any help is greatly appreciated. Thanks Ulf --- galaxy.jobs.handler ERROR 2014-10-07 10:32:24,676 Exception in monitor_step Traceback (most recent call last): File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py, line 161, in __monitor self.__monitor_step() File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py, line 184, in __monitor_step hda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \ File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py, line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py, line 1088, in query return self._query_cls(entities, self, **kwargs) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 108, in __init__ self._set_entities(entities) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 117, in _set_entities self._setup_aliasizers(self._entities) File /phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 132, in _setup_aliasizers _entity_info(entity) File
Re: [galaxy-dev] Disk space issue - again
Hi Viren, There's a script shipped with galaxy that you can use './scripts/set_user_disk_usage.py' to force recalculation of a user's disk usage. -Dannon On Tue, Sep 30, 2014 at 7:44 PM, Patel, Viren viren.pa...@emory.edu wrote: Hello. I have a Galaxy user whose disk usage remains at 91% even after deleting and purging all histories and datasets (The initial disk usage was 99%). I have searched the mailing list (e.g. http://dev.list.galaxyproject.org/disk-space-usage-td4660164.html) and wiki posts and followed all the steps, including purging hidden data. I have the cleanup scripts running once a day via cron: 01 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -1 11 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -2 21 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -4 31 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -5 41 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -3 51 01 * * * cd ~/galaxy-dist python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -6 01 02 * * * find ~/tmp -mtime +60 -delete I have manually run the above commands with -d 1 to delete anything older than 1 day and I have restarted the Galaxy service. However the user¹s disk usage remains at 91%. I am at a loss of what to try next. Any suggestions or ideas of what the issue could be, or what I need to do additionally? I am running the April 2014 distribution of Galaxy. Thanks. Viren This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] IE 11 issues
Hey all, This fix is in the galaxy-central, but does not exist in galaxy-dist yet. It will in the next release, and hopefully this is resolved for you at that point. -Dannon On Wed, Sep 24, 2014 at 1:40 PM, Sajdak, Doris dj...@buffalo.edu wrote: I tried using IE 11.0.9600.17280 and updated to the latest Galaxy but am still having the problems listed below. It’s not a big deal for us – we’ve just told users not to use IE. Dori ** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu ** *From:* Dannon Baker [mailto:dannon.ba...@gmail.com] *Sent:* Friday, September 19, 2014 6:29 AM *To:* Lukasse, Pieter *Cc:* Carl Eberhard; Sajdak, Doris; galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] IE 11 issues Hi Pieter, I updated the jQuery library that ships with galaxy in revision 14425:068fa60b8c2b on August 19, which should hopefully have resolved these issues. Are you still seeing problems on a galaxy server updated past that revision? -Dannon On Fri, Sep 19, 2014 at 4:45 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Carl, Any news on this? Thanks, Pieter. *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Carl Eberhard *Sent:* dinsdag 29 juli 2014 16:35 *To:* Sajdak, Doris *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] IE 11 issues That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris dj...@buffalo.edu wrote: Hi Carl, Thanks for the help. Here’s what I get when I try to upload a new file: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: '$' is undefined File: tool_runner, Line: 64, Column: 13 SCRIPT5007: Unable to get property 'extend' of undefined or null reference File: galaxy.panels.js, Line: 28, Column: 1 SCRIPT5002: Function expected File: tool_runner, Line: 80, Column: 5 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 SCRIPT5002: Function expected File: galaxy.tools.js, Line: 9, Column: 5 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 I get the following when I click on the edit button next to one of the items in my history: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: 'jQuery' is undefined File: jquery.autocomplete.js, Line: 9, Column: 2 SCRIPT5009: 'jQuery' is undefined File: galaxy.autocom_tagging.js, Line: 20, Column: 1 SCRIPT5009: '$' is undefined File: edit, Line: 528, Column: 9 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 This is what I get from ‘hg summary:’ parent: 12442:29ce93a13ac7 tip Merge stable branch. branch: default commit: 1 modified, 177 unknown update: (current) Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s something wrong on my end. Thanks, Dori *From:* Carl Eberhard [mailto:carlfeberh...@gmail.com] *Sent:* Monday, July 28, 2014 10:55 AM *To:* Björn Grüning *Cc:* galaxy-dev@lists.bx.psu.edu; Sajdak, Doris *Subject:* Re: [galaxy-dev] IE 11
Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
Hi Julie! The action resolves at the completion time of the job it is attached to, deleting datasets of any other already-completed jobs in that workflow which are not marked as an output step (with a highlighted snowflake). This will *not* delete datasets of any job marked as an output. Perhaps the confusion is that they're also marked as 'hidden' since they are not output steps? The general use-case for this is to put it on one of the 'final' steps of a workflow (or multiple if you have a workflow with two long parallel tracks) to clean up and delete datasets from intermediate jobs (which have already completed) that you don't want to save as an output. -Dannon On Tue, Sep 23, 2014 at 4:03 AM, julie dubois dubju...@gmail.com wrote: Hi all, I'm not sure how do this post-action act . I've been make some test and it's very confused for me. First, can this post-action be used on output which are used on other steps of the workflow ? if yes, I suppose that galaxy wait for end of use of this output before deleting. Second, must I higlight the snowfalke of this output to permit its deletion or must I keep the snowflake in grey ? I post this question in galaxy-dev because I've added this post-action on several outputs in my workflow and it has had no effect on my outputs. And when I open the .ga file which describe my workflow, I've seen just one of this post-action in one output. Thanks. Julie ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
Hi Julie,
You don't attach the 'Delete Intermediate Datasets' action to a dataset you
want to delete -- you attach it to one of the 'final' output steps of your
workflow, at which point the action will clean up all datasets up to that
point.
So, for a simple example, see this workflow for selecting random FASTA
lines from FASTQ.
[image: Inline image 1]
Select random lines is flagged as an output step, and the Delete
Intermediates action is attached to it. When the workflow runs, the FASTQ
to FASTA step will be deleted.
More detail from the Run workflow page, showing the attached action:
[image: Inline image 2]
Does that help explain things?
-Dannon
On Tue, Sep 23, 2014 at 9:37 AM, julie dubois dubju...@gmail.com wrote:
Hi Dannon,
Thanks for your answer. Sorry but I think I don't understand all of
your explanations.
First : if an output is marked with a highlighted snowflake, it will
be not deleted : it's OK
Second : if a dataset is used in several steps of my workflow, it will
be deleted when all these steps will be terminated : it's OK
But : Perhaps the confusion is that they're also marked as 'hidden'
since they are not output steps?
I don't understand :
so in my mind, when the dataset is marked with a grey snowflake, it is
automatically hidden and it's translated in the file of the workflow
with this code :
post_job_actions: {
HideDatasetActionout_file1: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: out_file1
}
},
But when I add another postJobAction to such dataset , with this
translation in the workflow file :
post_job_actions: {
HideDatasetActionout_file1: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: out_file1
},
DeleteIntermediatesActionout_file1: {
action_arguments: {},
action_type: DeleteIntermediatesAction,
output_name: out_file1
}
},
The result in my history is an hidden dataset (visible when I chek the
hisotry option include hidden dataset) but not a deleted dataset
(visible when I chek the history option include deleted datasets)
And it is the case for datasets used in several steps of workflow AND
for dataset which is just an output of a job not used in an other job.
Is an hidden dataset not deletable ?
I've changed the order of postJobActions in the file, but no effect.
And If I remove the HideDatasetAction, the dataset is not removed
because it become marked with highligthed snowflake.
So is your final purpose the alone solution to delete intermediates
datasets ? And if I correctly understand, I must create a tool that
take all my deletable datasets as input and which will remove all of
these. In this case, the postJobAction DeleteIntermediates is not
usefull, is it ?
Thanks.
Julie
2014-09-23 14:15 GMT+02:00 Dannon Baker dannon.ba...@gmail.com:
Hi Julie!
The action resolves at the completion time of the job it is attached to,
deleting datasets of any other already-completed jobs in that workflow
which
are not marked as an output step (with a highlighted snowflake). This
will
*not* delete datasets of any job marked as an output.
Perhaps the confusion is that they're also marked as 'hidden' since they
are
not output steps?
The general use-case for this is to put it on one of the 'final' steps
of a
workflow (or multiple if you have a workflow with two long parallel
tracks)
to clean up and delete datasets from intermediate jobs (which have
already
completed) that you don't want to save as an output.
-Dannon
On Tue, Sep 23, 2014 at 4:03 AM, julie dubois dubju...@gmail.com
wrote:
Hi all,
I'm not sure how do this post-action act . I've been make some test
and it's very confused for me.
First, can this post-action be used on output which are used on other
steps of the workflow ? if yes, I suppose that galaxy wait for end of
use of this output before deleting.
Second, must I higlight the snowfalke of this output to permit its
deletion or must I keep the snowflake in grey ?
I post this question in galaxy-dev because I've added this
post-action on several outputs in my workflow and it has had no effect
on my outputs. And when I open the .ga file which describe my
workflow, I've seen just one of this post-action in one output.
Thanks.
Julie
___
Please keep all replies on the list by using reply all
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and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
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http://galaxyproject.org/search/mailinglists
Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput
Can you show me a screenshot or json output of the workflow?
Situations where the delete intermediates action wouldn't delete a dataset
are:
1) Subsequent job that has not finished still needs that dataset.
2) Dataset is marked as an output.
3) The job that creates the dataset isn't finished at the time of the
processing of the delete intermediates action.
There's a log message that you'd see (in your system galaxy log) if the
dataset state is detected as unfinished, something like Workflow
Intermediates cleanup attempted, but non terminal state...
On Tue, Sep 23, 2014 at 10:33 AM, julie dubois dubju...@gmail.com wrote:
OK!!! Thanks it's more clear for me.
So I've a bug!
I've followed your instructions. the DeleteAction is attached to the final
step of my workflow. Before this, 2 steps exist with one output dataset not
marked as output of workflow for each of this 2 step.
The dataset of my first step is hidden and deleted : good!
But the dataset of my second step is hidden but not deleted ! I don't
understand why
Thanks
Julie
2014-09-23 15:49 GMT+02:00 Dannon Baker dannon.ba...@gmail.com:
Hi Julie,
You don't attach the 'Delete Intermediate Datasets' action to a dataset
you want to delete -- you attach it to one of the 'final' output steps of
your workflow, at which point the action will clean up all datasets up to
that point.
So, for a simple example, see this workflow for selecting random FASTA
lines from FASTQ.
[image: Inline image 1]
Select random lines is flagged as an output step, and the Delete
Intermediates action is attached to it. When the workflow runs, the FASTQ
to FASTA step will be deleted.
More detail from the Run workflow page, showing the attached action:
[image: Inline image 2]
Does that help explain things?
-Dannon
On Tue, Sep 23, 2014 at 9:37 AM, julie dubois dubju...@gmail.com wrote:
Hi Dannon,
Thanks for your answer. Sorry but I think I don't understand all of
your explanations.
First : if an output is marked with a highlighted snowflake, it will
be not deleted : it's OK
Second : if a dataset is used in several steps of my workflow, it will
be deleted when all these steps will be terminated : it's OK
But : Perhaps the confusion is that they're also marked as 'hidden'
since they are not output steps?
I don't understand :
so in my mind, when the dataset is marked with a grey snowflake, it is
automatically hidden and it's translated in the file of the workflow
with this code :
post_job_actions: {
HideDatasetActionout_file1: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: out_file1
}
},
But when I add another postJobAction to such dataset , with this
translation in the workflow file :
post_job_actions: {
HideDatasetActionout_file1: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: out_file1
},
DeleteIntermediatesActionout_file1: {
action_arguments: {},
action_type: DeleteIntermediatesAction,
output_name: out_file1
}
},
The result in my history is an hidden dataset (visible when I chek the
hisotry option include hidden dataset) but not a deleted dataset
(visible when I chek the history option include deleted datasets)
And it is the case for datasets used in several steps of workflow AND
for dataset which is just an output of a job not used in an other job.
Is an hidden dataset not deletable ?
I've changed the order of postJobActions in the file, but no effect.
And If I remove the HideDatasetAction, the dataset is not removed
because it become marked with highligthed snowflake.
So is your final purpose the alone solution to delete intermediates
datasets ? And if I correctly understand, I must create a tool that
take all my deletable datasets as input and which will remove all of
these. In this case, the postJobAction DeleteIntermediates is not
usefull, is it ?
Thanks.
Julie
2014-09-23 14:15 GMT+02:00 Dannon Baker dannon.ba...@gmail.com:
Hi Julie!
The action resolves at the completion time of the job it is attached
to,
deleting datasets of any other already-completed jobs in that workflow
which
are not marked as an output step (with a highlighted snowflake). This
will
*not* delete datasets of any job marked as an output.
Perhaps the confusion is that they're also marked as 'hidden' since
they are
not output steps?
The general use-case for this is to put it on one of the 'final' steps
of a
workflow (or multiple if you have a workflow with two long parallel
tracks)
to clean up and delete datasets from intermediate jobs (which have
already
completed) that you don't want to save as an output.
-Dannon
On Tue, Sep 23, 2014 at 4:03
Re: [galaxy-dev] IE 11 issues
Hi Pieter, I updated the jQuery library that ships with galaxy in revision 14425:068fa60b8c2b on August 19, which should hopefully have resolved these issues. Are you still seeing problems on a galaxy server updated past that revision? -Dannon On Fri, Sep 19, 2014 at 4:45 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Carl, Any news on this? Thanks, Pieter. *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Carl Eberhard *Sent:* dinsdag 29 juli 2014 16:35 *To:* Sajdak, Doris *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] IE 11 issues That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using either Chrome/Firefox or an older version of IE (10?). You might also try using IE's compatibility mode but this must be set on a per browser basis and might be tedious: https://kb.wisc.edu/page.php?id=35591 I'll update when I find out more and thanks for the report, Carl On Mon, Jul 28, 2014 at 1:24 PM, Sajdak, Doris dj...@buffalo.edu wrote: Hi Carl, Thanks for the help. Here’s what I get when I try to upload a new file: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: '$' is undefined File: tool_runner, Line: 64, Column: 13 SCRIPT5007: Unable to get property 'extend' of undefined or null reference File: galaxy.panels.js, Line: 28, Column: 1 SCRIPT5002: Function expected File: tool_runner, Line: 80, Column: 5 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 SCRIPT5002: Function expected File: galaxy.tools.js, Line: 9, Column: 5 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 SCRIPT70: Permission denied File: root, Line: 1182, Column: 2 I get the following when I click on the edit button next to one of the items in my history: SCRIPT438: Object doesn't support property or method 'attachEvent' File: jquery.js, Line: 1514, Column: 3 SCRIPT5009: 'jQuery' is undefined File: jquery.migrate.js, Line: 6, Column: 2 SCRIPT5009: 'jQuery' is undefined File: select2.js, Line: 21, Column: 2 SCRIPT5007: Unable to get property 'fn' of undefined or null reference File: bootstrap.js, Line: 44, Column: 3 SCRIPT5009: '$' is undefined File: galaxy.base.js, Line: 52, Column: 1 SCRIPT5009: 'jQuery' is undefined File: ui.js, Line: 735, Column: 5 SCRIPT5009: 'jQuery' is undefined File: jquery.autocomplete.js, Line: 9, Column: 2 SCRIPT5009: 'jQuery' is undefined File: galaxy.autocom_tagging.js, Line: 20, Column: 1 SCRIPT5009: '$' is undefined File: edit, Line: 528, Column: 9 SCRIPT438: Object doesn't support property or method 'attachEvent' File: root, Line: 1514, Column: 3 This is what I get from ‘hg summary:’ parent: 12442:29ce93a13ac7 tip Merge stable branch. branch: default commit: 1 modified, 177 unknown update: (current) Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s something wrong on my end. Thanks, Dori *From:* Carl Eberhard [mailto:carlfeberh...@gmail.com] *Sent:* Monday, July 28, 2014 10:55 AM *To:* Björn Grüning *Cc:* galaxy-dev@lists.bx.psu.edu; Sajdak, Doris *Subject:* Re: [galaxy-dev] IE 11 issues Hi, Dori Galaxy supports IE 10+ so this is definitely a bug. I'm checking for bugs in the history panel now, but in the meantime: - can you open the javascript console in your IE and see if any errors are displayed when doing the two tasks you mention? http://msdn.microsoft.com/en-us/library/ie/bg182326%28v=vs.85%29.aspx - What version of Galaxy does your lab use currently? (You can view the version by using the 'hg summary' command from the directory from which Galaxy is run) As an aside, IE has traditionally veered away from web standards and made it difficult to program compatible sites. Recent versions of IE have become much more standards compliant allowing us to support them well enough. Please don't hesitate to report IE (10+) bugs when using Galaxy. Thanks for the report and I'll update with my findings soon, Carl On Mon, Jul 28, 2014 at 10:42 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Dori, the IE is not really
Re: [galaxy-dev] Workflow param error leads to template error [patch]
Hi Tim, Thanks for this. If you still have it handy, what was the exact attribute error? -Dannon On Thu, Sep 18, 2014 at 10:28 AM, Tim Booth tbo...@ceh.ac.uk wrote: Dear Devs, I recently ran into a problem where attempting to run a workflow resulted in an uninformative error and a traceback in the logs, that I put into Google. This led me to the message below from 2012. As far as I can see it got no reply at the time and I have hit the same issue. I modified database/compiled_templates/workflow/run.mako.py and this resulted in a much more useful error report appearing in the browser. Obviously this is a generated file, so attached is a patch for templates/webapps/galaxy/workflow/run.mako that I propose you add to Galaxy. As you'll see it just adds a single try block and then ignores the exception, which I would say in this case is not actually a bad thing to do even if it is not the ideal fix. Should be fairly explanatory from the patch. Cheers, TIM Way way back in Jun 2012, Paul-Michael.Agapow at hpa.org.uk wrote: Looking for pointers on what might be causing this problem: A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends: Module workflow_run_mako:232 in render_body for ic in oc.input_step.module.get_data_inputs(): AttributeError: 'WorkflowStep' object has no attribute 'module' After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render run.mako flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring? Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't) Hosting OS: CentOS 6 -- Paul Agapow (paul-michael.agapow at hpa.org.uk) Bioinformatics, Health Protection Agency (UK) -- Tim Booth tbo...@ceh.ac.uk NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about uploading a large application to the tool-shed
Hi George, I'd think something is a bit wonky if it needs to be that big. Mind sharing what's in there and why it needs to be so large? -Dannon On Wed, Sep 17, 2014 at 4:59 PM, George Weingart george.weing...@gmail.com wrote: Hello, I have an application that is working perfectly in our local Galaxy (Not using tool-shed) I would like to upload it to the tool-shed (I have uploaded other applications to the tool-shed before) The size of the directory (//usr/local/galaxy-dist/tools/metaphlan2) is 2.1 GB and after I tar it it is 1.1 GB. The question: Is it too big to be uploaded to the tool-shed? Thanks! George Weingart ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0
Hey Ashish, We have an open issue to sort out exactly why/how this happens, but a quick fix for many users is just to remove your eggs/ folder and all eggs and re-run `python scripts/fetch_eggs.py`. Give that a shot, but do let me know if it doesn't' work. On Wed, Sep 10, 2014 at 4:54 PM, ashish damania ashis...@hotmail.com wrote: # sh run.sh Some eggs are out of date, attempting to fetch...Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be downloaded automatically. You can trybuilding it by hand with: python scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call last): File /usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line 38, in app_factory from galaxy.app import UniverseApplication File /usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py, line 12, in module from galaxy.visualization.data_providers.registry import DataProviderRegistry File /usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py, line 2, in module from galaxy.visualization.data_providers import genome File /usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 17, in module from pysam import ! csamtools, ctabix File /usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/pysam/__init__.py, line 1, in module from csamtools import *ImportError: /usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/csamtools.so: Undefined symbol __ks_insertsort_heap So I have tried running this script python scripts/scramble.py -e simplejson Traceback (most recent call last): File scripts/scramble.py, line 50, in module egg.scramble() File /usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/scramble.py, line 60, in scramble raise ScrambleFailure( self, %s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s % ( sys._getframe().f_code.co_name, self.name, new_egg ) )galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson did not appear to fail, but no egg found to copy from expected path: /usr/home/ec2-user/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.egg I found that I have file named: simplejson-2.1.1-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg in the ../scripts/scramble/build/py2.7/simplejson/dist/ folder. I renamed that file simplejson-2.1.1-py2.7.egg but it gives me that same error when I execute sh run.sh. Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility issues? Thanks you. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem uploading files to RNA-Rocket
Hey David, I'm not sure why you'd be having this issue, but I'd contact the RNA-Rocket server staff (pathporth...@vbi.vt.edu) for more assistance; this is not a Galaxy server that the Galaxy Team manages. -Dannon On Thu, Aug 21, 2014 at 9:51 AM, David Salcines davidsalci...@gmail.com wrote: Hi, I was trying to upload some FASTQ files via FTP using the FileZilla client but although the program connects to the server it doesn't log in. I checked the user and the password several times and I tried to use another account but I still got the same error. I also tried to upload the files via URL (using Mega) but when the upload is finished the files appear to be empty. Thanks David ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] bioblend run_workflow (no_wait?)
There is no reason workflow invocation *has* to be synchronous, but that's how galaxy works right now as, mostly, a historical artifact. Workflow scheduling happens inside the web request, and other than bioblend issuing the request in another thread there won't be an implementation w/ no_wait. This is definitely suboptimal, and backgrounded (among other enhancements to scheduling) workflow invocation is something we're working on right now, and it's a high priority. On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig boll0...@umn.edu wrote: I'm using bioblend to launch a workflow, but i find that the gi.workflows.run_workflow() command does not provide an option for no_wait. Can anyone provide justification for why this needs to be synchronous? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] bioblend run_workflow (no_wait?)
So, see the commentary on the bioblend issue you added as well, but in short -- while you should currently expect to wait while the entire workflow was queued, bioblend *should not* be blocking waiting for all jobs to complete and that sounds like a bioblend bug if it is. That's what the 'wait' param is for after all. On Thu, Aug 21, 2014 at 5:27 PM, Evan Bollig boll0...@umn.edu wrote: Thanks Dannon. Looking forward to the resolution. We've got some long workflows (100+ steps) that take days to compute. It takes about 2 minutes to finish queuing tasks, and then I found that they continue to execute even if I interrupt the bioblend thread. I'll add a signal.alarm interrupt to kill the bioblend thread and continue manual monitoring. -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Thu, Aug 21, 2014 at 4:20 PM, Dannon Baker dannon.ba...@gmail.com wrote: There is no reason workflow invocation *has* to be synchronous, but that's how galaxy works right now as, mostly, a historical artifact. Workflow scheduling happens inside the web request, and other than bioblend issuing the request in another thread there won't be an implementation w/ no_wait. This is definitely suboptimal, and backgrounded (among other enhancements to scheduling) workflow invocation is something we're working on right now, and it's a high priority. On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig boll0...@umn.edu wrote: I'm using bioblend to launch a workflow, but i find that the gi.workflows.run_workflow() command does not provide an option for no_wait. Can anyone provide justification for why this needs to be synchronous? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow Loop
It's currently not possible to build loops into galaxy workflows. Major workflow engine enhancements are being worked on, but for an immediate solution you could drive something like this using the API if you wanted to. -Dannon On Thu, Aug 14, 2014 at 8:54 AM, Görkem Erdoğan gorkemerdoga...@gmail.com wrote: Hello All, I have a little issue. I want create workflow with loop but workflow's nodes must use different settings in each loop steps.How can i do this? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy server broken with install of latest changes
Thanks for the update, glad everything is working as expected! On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik kusa...@cs.usask.ca wrote: My apologies to everyone. This turns out to be a false alarm. The problem was caused by a strange, intermittent issue with the DNS servers on our campus (I'll spare you the gory details). The problem boiled down to python on my server not being able to find http://eggs.galaxyproject.org. On Aug 12, 2014, at 13:13 , Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes were waiting to be applied, changeset 13772 through changeset 14309. Fine. I did hg pull -u and got searching for changes adding changesets adding manifests adding file changes added 538 changesets with 1738 changes to 542 files 473 files updated, 0 files merged, 152 files removed, 0 files unresolved Fine. However, now my Galaxy server will not start up and run. On sh run.sh --daemon the server dies with the following produced in paster.log where /birl2/Galaxy/galaxy-dist is the name of the installation directory. -- begin paster.log -- Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 49, in run invoke(command, command_name, options, args[1:]) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 55, in invoke exit_code = runner.run(args) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 22 0, in run result = self.command() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 64 3, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /birl2/Galaxy/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py, line 4, in modul e from framework import expose File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py, line 48 , in module eggs.require( amqp ) File /birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 414, in req uire raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['amqp'] Removing PID file paster.pid -- end paster.log -- The above is the complete content of paster.log. Anyone have any idea what the problem is? More importantly, how do I fix the problem and get Galaxy running again? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at:
Re: [galaxy-dev] bug?
2721 postgresql-Wed.log: 2014-08-06 15:01:59.911 EDT ERROR: invalid input syntax for integer: 669c887f39dcb67f at character 2721 postgresql-Wed.log: 2014-08-06 15:04:26.964 EDT ERROR: invalid input syntax for integer: a328cf0b6432c591 at character 2721 postgresql-Wed.log: 2014-08-06 15:20:06.512 EDT ERROR: invalid input syntax for integer: dcdc4c79298533e4 at character 2721 postgresql-Wed.log: 2014-08-06 15:22:41.220 EDT ERROR: invalid input syntax for integer: 054cf6e4a4f90798 at character 2721 postgresql-Wed.log: 2014-08-06 15:25:22.955 EDT ERROR: invalid input syntax for integer: 054cf6e4a4f90798 at character 2721 postgresql-Wed.log: 2014-08-06 15:44:16.015 EDT ERROR: invalid input syntax for integer: 054cf6e4a4f90798 at character 2721 postgresql-Wed.log: 2014-08-06 15:44:26.196 EDT ERROR: invalid input syntax for integer: d9e57b7bae035246 at character 2721 postgresql-Wed.log: 2014-08-06 15:45:03.724 EDT ERROR: invalid input syntax for integer: d9e57b7bae035246 at character 2721 -- Brad Langhorst, Ph.D. Applications and Product Development Scientist On Aug 8, 2014, at 10:40 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Brad, So I've dug around and replicated all the requests in the web log you sent (central#default tip -- what revision are you running?), but I'm not seeing any unencoded id queries my sql logs (expected this more or less, w/ all of the requests in your web log being 200 OK's). The next guess is that it has to do with job metrics or metadata. The job itself failed, do you know why that is? What job metrics do you have enabled? And has this been a consistent issue, or you just happened to notice the error this one time? -Dannon On Tue, Aug 5, 2014 at 5:53 PM, Langhorst, Brad langho...@neb.com wrote: I tried to do some time correlation between galaxy logs and postgres logs… postgres 2014-08-01 17:15:15.643 EDT handler1.log galaxy.jobs.output_checker INFO 2014-08-01 17:15:08,875 Job 123681: Fatal error: Exit code 1 (Interval subtraction error) galaxy.jobs DEBUG 2014-08-01 17:15:08,948 setting dataset state to ERROR galaxy.jobs INFO 2014-08-01 17:15:09,196 Collecting job metrics for galaxy.model.Job object at 0x7fcbacccbb50 galaxy.jobs DEBUG 2014-08-01 17:15:09,208 job 123681 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:15:09,208 Cleaning up external metadata files galaxy.jobs.runners.drmaa DEBUG 2014-08-01 17:17:32,338 (123678/1521440) state change: job finished normally handler0.log laxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,572 loading metadata from file for: HistoryDatasetAssociation 192134 galaxy.jobs INFO 2014-08-01 17:14:40,804 Collecting job metrics for galaxy.model.Job object at 0x7f15fc281850 galaxy.jobs DEBUG 2014-08-01 17:14:40,815 job 123680 ended galaxy.datatypes.metadata DEBUG 2014-08-01 17:14:40,815 Cleaning up external metadata files python path is: /mnt/galaxy/data/galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/anyjson-0.3.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Babel-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/pytz-2013.9-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /mnt/galaxy/data/galaxy/galaxy-dist/lib, /mnt/galaxy/data/galaxy/sw/lib/python2.7/site-packages/cutadapt-1.3-py2.7-linux-x86_64.egg, /mnt/galaxy/data
Re: [galaxy-dev] Galaxy server broken with install of latest changes
Hey Tony, Thanks for the error report. I'll look into this, but you can try two things really quickly to see if you can get galaxy started: 1) python scripts/fetch_eggs.py may fix up your egg situation 2) just delete the eggs folder of your galaxy distribution (galaxy-dist/eggs) and start galaxy again. It'll automatically fetch everything it needs. -Dannon On Tue, Aug 12, 2014 at 3:13 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes were waiting to be applied, changeset 13772 through changeset 14309. Fine. I did hg pull -u and got searching for changes adding changesets adding manifests adding file changes added 538 changesets with 1738 changes to 542 files 473 files updated, 0 files merged, 152 files removed, 0 files unresolved Fine. However, now my Galaxy server will not start up and run. On sh run.sh --daemon the server dies with the following produced in paster.log where /birl2/Galaxy/galaxy-dist is the name of the installation directory. -- begin paster.log -- Traceback (most recent call last): File ./scripts/paster.py, line 33, in module serve.run() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 49, in run invoke(command, command_name, options, args[1:]) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 10 55, in invoke exit_code = runner.run(args) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 22 0, in run result = self.command() File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line 64 3, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 374, in loadobj global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 399, in loadcontext global_conf=global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 561, in get_context section) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 620, in _context_from_explicit value = import_string(found_expr) File /birl2/Galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py, line 125, in import_string return pkg_resources.EntryPoint.parse(x= + s).load(False) File /birl2/Galaxy/galaxy-dist/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/__init__.py, line 4, in modul e from framework import expose File /birl2/Galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py, line 48 , in module eggs.require( amqp ) File /birl2/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 414, in req uire raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['amqp'] Removing PID file paster.pid -- end paster.log -- The above is the complete content of paster.log. Anyone have any idea what the problem is? More importantly, how do I fix the problem and get Galaxy running again? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] sql server timeout
Hi Don, Haven't seen this before myself, but I did a little digging here: http://docs.sqlalchemy.org/en/rel_0_8/faq.html#mysql-server-has-gone-away So, to differentiate between those two issues, does this happen very frequently or only after a long idle? -Dannon On Wed, Aug 6, 2014 at 3:15 PM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: On occasion I'm getting and 'Internal Server error' on login with my production galaxy server. If I refresh the page I'm able to login just fine. This instance of galaxy has an apache frontend and a mysql server on the back end. If I look at my log files I see: OperationalError: (OperationalError) (2006, 'MySQL server has gone away') 'SELECT galaxy_session.id AS galaxy_session_id. It looks like perhaps galaxy is trying to use a stale session or something like that. Has anyone else seen this problem and is there an easy solution aside from having users refresh the page? Thanks, Don FSU Research Computing Center ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] bug?
:15:10 -0400] GET /datasets/49b19822485c7897/display/?preview=True HTTP/1.0 200 - http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36 172.17.130.113 - - [01/Aug/2014:17:15:11 -0400] GET /datasets/49b19822485c7897/show_params HTTP/1.0 200 - http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36 172.17.130.113 - - [01/Aug/2014:17:15:12 -0400] GET /api/histories/39a249c523d1b262 HTTP/1.0 200 - http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36 172.17.130.113 - - [01/Aug/2014:17:15:15 -0400] GET /dataset/errors?id=49b19822485c7897 HTTP/1.0 200 - http://galaxy.neb.com/root/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.125 Safari/537.36 -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 5:18 PM, Dannon Baker dannon.ba...@gmail.com wrote: Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad langho...@neb.com wrote: I see this in my database server logs… SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists
Re: [galaxy-dev] ToolShed error: samtools installation failure
That's correct -- none of them are run automatically. On Wed, Aug 6, 2014 at 3:08 PM, Beginner TI ruiwang...@gmail.com wrote: Ah, I think that I had a wrong impression before...so by default, the migration scripts listed here will NOT be executed, am I correct? I think that 'done' at the bottom made me think that it was executed... So it's the user's responsibility to execute those scripts, correct? Thanks, Rui The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed fromdatatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. Therepositories named emboss_5 and emboss_datatypes from the main Galaxy Tool Shed at http://toolshed.g2.bx.psu.eduwill be installed into your local Galaxy instance at the location discussed above by running the following command.vsh ./scripts/migrate_tools/0002_tools.sh^doneAfter the installation process finishes, you can start your Galaxy server. As part of this installation process,entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so thesetools will continue to be loaded into your tool panel. Because of this, existing entries for these files should beremoved from your file named ./tool_conf.xml, but only after the installation process finishes. On Wed, Aug 6, 2014 at 10:53 AM, Dannon Baker dannon.ba...@gmail.com wrote: Ahh, I think I see the issue. So, many galaxy tools are being migrated out of the distribution and to the toolshed -- you can find much more detailed information here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution The samtools wrappers were migrated in migration 8, I think, if that helps. Basically, there's a migration script that should have shown up in a terminal somewhere when you ran your galaxy instance after the update that will contain a reference to script(s) that you can run that'll take care of the migration. Let me know if you need more information, if the wiki page doesn't clear it up! -Dannon On Wed, Aug 6, 2014 at 1:36 PM, Beginner TI ruiwang...@gmail.com wrote: Hi Dannon, Thanks for the reply. Sorry for the duplicate. I was wondering that the original subject sounded like a user problem so I updated it... Actually we are having a little down time right now for a file system check. I'll try your suggestions asap and let you know. At the mean time, could you please elaborate this a little bit? I noticed that in the tool_conf.xml, not every tool is shown on the panel although they are all defined there in the same format. I also noticed that all the tool xml files, such as section id=samtools name=NGS: SAM Tools tool file=samtools/sam_bitwise_flag_filter.xml / tool file=samtools/sam2interval.xml / tool file=samtools/sam_to_bam.xml / tool file=samtools/bam_to_sam.xml / tool file=samtools/sam_merge.xml / tool file=samtools/samtools_mpileup.xml / tool file=samtools/sam_pileup.xml / tool file=samtools/pileup_parser.xml / tool file=samtools/pileup_interval.xml / tool file=samtools/samtools_flagstat.xml / tool file=samtools/samtools_rmdup.xml / tool file=samtools/samtools_slice_bam.xml / /section the directory samtools and all these xml files are no longer in the tools directory. seems that upgrade deleted them. is this correct? or they are moved to somewhere else? I looked around but didn't see. Based on this, I think that even I removed the tool_panel.xml file you mentioned, I will still not be able to restore samtools even I could see it...could you please let me know how I could configure this? Thanks, Rui On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Rui, We'll definitely take a look. Please allow for a reasonable time period to pass before sending duplicate emails to the list asking for assistance. That said, does deleting your integrated_tool_panel.xml (this file is automatically regenerated by Galaxy, safe to remove it and restart) bring back your manually installed samtools? On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI ruiwang...@gmail.com wrote: Could someone please take a look? Thanks, Rui On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI ruiwang...@gmail.com wrote: Dear Admin, Since the upgrade, I lost the samtools that I installed myself. Although it is still in the tool_conf.xml, it does not show up on the panel. I tried to install from toolshed, but failed. Error messages pasted below. Could someone take a look? Thanks, Rui ⇝ AttributeError: 'NoneType' object has no attribute 'strip' URL: http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977 Module
Re: [galaxy-dev] ToolShed error: samtools installation failure
Hi Rui, We'll definitely take a look. Please allow for a reasonable time period to pass before sending duplicate emails to the list asking for assistance. That said, does deleting your integrated_tool_panel.xml (this file is automatically regenerated by Galaxy, safe to remove it and restart) bring back your manually installed samtools? On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI ruiwang...@gmail.com wrote: Could someone please take a look? Thanks, Rui On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI ruiwang...@gmail.com wrote: Dear Admin, Since the upgrade, I lost the samtools that I installed myself. Although it is still in the tool_conf.xml, it does not show up on the panel. I tried to install from toolshed, but failed. Error messages pasted below. Could someone take a look? Thanks, Rui ⇝ AttributeError: 'NoneType' object has no attribute 'strip' URL: http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977 Module weberror.evalexception.middleware:*364* in respond http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.recursive:*84* in __call__ http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# body *=* method*(* trans*,* kwargs *)* Module galaxy.web.framework:*369* in decorator http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# *return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*983* in prepare_for_install
Re: [galaxy-dev] ToolShed error: samtools installation failure
Ahh, I think I see the issue. So, many galaxy tools are being migrated out of the distribution and to the toolshed -- you can find much more detailed information here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution The samtools wrappers were migrated in migration 8, I think, if that helps. Basically, there's a migration script that should have shown up in a terminal somewhere when you ran your galaxy instance after the update that will contain a reference to script(s) that you can run that'll take care of the migration. Let me know if you need more information, if the wiki page doesn't clear it up! -Dannon On Wed, Aug 6, 2014 at 1:36 PM, Beginner TI ruiwang...@gmail.com wrote: Hi Dannon, Thanks for the reply. Sorry for the duplicate. I was wondering that the original subject sounded like a user problem so I updated it... Actually we are having a little down time right now for a file system check. I'll try your suggestions asap and let you know. At the mean time, could you please elaborate this a little bit? I noticed that in the tool_conf.xml, not every tool is shown on the panel although they are all defined there in the same format. I also noticed that all the tool xml files, such as section id=samtools name=NGS: SAM Tools tool file=samtools/sam_bitwise_flag_filter.xml / tool file=samtools/sam2interval.xml / tool file=samtools/sam_to_bam.xml / tool file=samtools/bam_to_sam.xml / tool file=samtools/sam_merge.xml / tool file=samtools/samtools_mpileup.xml / tool file=samtools/sam_pileup.xml / tool file=samtools/pileup_parser.xml / tool file=samtools/pileup_interval.xml / tool file=samtools/samtools_flagstat.xml / tool file=samtools/samtools_rmdup.xml / tool file=samtools/samtools_slice_bam.xml / /section the directory samtools and all these xml files are no longer in the tools directory. seems that upgrade deleted them. is this correct? or they are moved to somewhere else? I looked around but didn't see. Based on this, I think that even I removed the tool_panel.xml file you mentioned, I will still not be able to restore samtools even I could see it...could you please let me know how I could configure this? Thanks, Rui On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Rui, We'll definitely take a look. Please allow for a reasonable time period to pass before sending duplicate emails to the list asking for assistance. That said, does deleting your integrated_tool_panel.xml (this file is automatically regenerated by Galaxy, safe to remove it and restart) bring back your manually installed samtools? On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI ruiwang...@gmail.com wrote: Could someone please take a look? Thanks, Rui On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI ruiwang...@gmail.com wrote: Dear Admin, Since the upgrade, I lost the samtools that I installed myself. Although it is still in the tool_conf.xml, it does not show up on the panel. I tried to install from toolshed, but failed. Error messages pasted below. Could someone take a look? Thanks, Rui ⇝ AttributeError: 'NoneType' object has no attribute 'strip' URL: http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977 Module weberror.evalexception.middleware:*364* in respond http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.recursive:*84* in __call__ http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977# view http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu
Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy
The method John suggests is definitely a better way to get the user's API
key.
That said, the 'get' change is due to sqlalchemy version changes that
happened quite a while back. You can no longer 'get' directly from the
model, you must use a query object. So, for example, this line:
model.User.get( id )
Became:
sa_session.query( self.model.User).get( id )
Hope that gives a little context,
-Dannon
On Tue, Aug 5, 2014 at 8:56 AM, John Chilton jmchil...@gmail.com wrote:
Hmm...
The following should work for the last at least three releases I
think: ${__user__.api_keys[0].key}. Not sure why get/find are
unavailable on the User model class in the cheetah template now. I
think this version is a little better. Is this okay? If not I can
create a Trello card to investigate and restore the old functionality.
-John
On Tue, Aug 5, 2014 at 2:26 AM, neil.burd...@csiro.au wrote:
Hi,
I have recently upgraded Galaxy from a version I had last year. In my
tool xml file I could state:
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
in the command section to get the user's API. However, after updating
to
the current version of Galaxy I get the following error when using this
entry in the xml file:
Traceback (most recent call last):
File /home/bmladmin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 153, in prepare_job
job_wrapper.prepare()
File /home/bmladmin/galaxy-dist/lib/galaxy/jobs/__init__.py, line
712,
in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
File /home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py, line
348, in build
self.__build_command_line( )
File /home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py, line
364, in __build_command_line
command_line = fill_template( command, context=param_dict )
File /home/bmladmin/galaxy-dist/lib/galaxy/util/template.py, line 9,
in
fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
/home/bmladmin/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
line 1004, in __str__
return getattr(self, mainMethName)()
File
cheetah_DynamicallyCompiledCheetahTemplate_1407207170_7_53169.py,
line 92, in respond
NotFound: cannot find 'get' while searching for 'get'
Any ideas?
Thanks
Neil
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Re: [galaxy-dev] Serious start-up delay in next-stable
There's definitely a request that will occasionally block at startup -- I've hit this before too, Martin. Looking into it now. On Tue, Aug 5, 2014 at 2:59 PM, Martin Čech mar...@bx.psu.edu wrote: I just freshly cloned galaxy-central, switched to next-stable and did initial startup - no problems detected and Galaxy booted in under 2m. On Tue, Aug 5, 2014 at 2:54 PM, Langhorst, Brad langho...@neb.com wrote: I’ve noticed that startup is very slow. It’s about 15 minutes for me to stop and restart my 4 daemons. It was much faster with galaxy on local storage. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 2:41 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi all, does anyone encountered a long start-up delay with the recent next-stable and starting a instance from scratch? For me its hanging at: tool_shed.galaxy_install.migrate.check DEBUG 2014-08-05 18:39:45,207 psycopg2 egg successfully loaded for postgres dialect for 3-5 minutes. Cheers, Bjoern ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] bug?
Definitely looks like an encoded id is being used in the query when it should be an unencoded id. I can try to dig through the query and make guesses as to what's calling it, but do you have any hints at all what's happening in galaxy at the time of this request? -Dannon On Tue, Aug 5, 2014 at 5:13 PM, Langhorst, Brad langho...@neb.com wrote: I see this in my database server logs… SELECT history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_a_1, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_d_2, history_dataset_association.hid AS history_dataset_association_hid, history_dataset_association.name AS history_dataset_association_name, history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_ins_3, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id, dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid FROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON dataset_1.id = history_dataset_association.dataset_id WHERE history_dataset_association.id = ‘49b19822485c7897' looks like a simple bug to me. But I don’t know an easy way to track it down. Any ideas? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] start and end times?
Hi Evan, What you're looking for should be covered by the new Job Metrics plugins. If you'd like to know more, see: https://wiki.galaxyproject.org/Admin/Config/JobMetrics -Dannon On Mon, Aug 4, 2014 at 3:24 PM, Evan Bollig boll0...@umn.edu wrote: Jobs executed in the workflow appear to have a creation time, but no execution start and end time listed. How does one determine when something executed? I'd like to know exactly where the time is spent computing... -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] start and end times?
These metrics would only apply to individual jobs and not for the entire history/workflow, though there are plans (https://trello.com/c/XsQdqliU) to expose the data via the API so that one might generate summary metrics, among other things. On Mon, Aug 4, 2014 at 3:40 PM, Evan Bollig boll0...@umn.edu wrote: Thanks Dannon. I'll add it to the todo list. Do the metric include time and memory info for the entire history/workflow, or does it only report for individual tools? Max consumed storage during a workflow execution is another data point I'd like to monitor. -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Mon, Aug 4, 2014 at 2:32 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Evan, What you're looking for should be covered by the new Job Metrics plugins. If you'd like to know more, see: https://wiki.galaxyproject.org/Admin/Config/JobMetrics -Dannon On Mon, Aug 4, 2014 at 3:24 PM, Evan Bollig boll0...@umn.edu wrote: Jobs executed in the workflow appear to have a creation time, but no execution start and end time listed. How does one determine when something executed? I'd like to know exactly where the time is spent computing... -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy won't start
Hi Dori,
If you haven’t updated galaxy or manipulated the eggs at all, then it might be
an updated system python module interfering with galaxy’s resolution of the
pyyaml we ship. Can you try running galaxy from an clean virtualenv?
(https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment)
If that’s not it, or you’d rather try something else, I’d probably suggest
wiping out galaxy’s eggs (or just moving the folder to eggs_backup or the like)
to force Galaxy to fetch all new eggs at the next restart, and see if that
resolves it.
-Dannon
On Jul 29, 2014, at 9:40 AM, Sajdak, Doris dj...@buffalo.edu wrote:
I’m suddenly getting this error today when I tried to restart Galaxy:
Starting galaxy...
Some eggs are out of date, attempting to fetch...
Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency bioblend requires pyyaml
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File /ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345,
in resolve
egg.resolve()
File /ifs/user/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 168,
in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /ifs/user/galaxy/galaxy-dist/lib/pkg_resources.py, line 569, in
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/ifs/user/galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('pyyaml'))
pyyaml is installed and I haven’t updated anything that would cause a
conflict. What do I do to fix this?
Thanks,
Dori
**
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu
**
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Re: [galaxy-dev] questions about cloudman
Hi Pablo, 1) I have read in the wiki that it's only available in region US East (Virginia). Will it be available in Ireland region? This is currently true, though we're hoping to mirror to other regions soon. 2) I see I need to attach EBS volumes to my head node to host the software and data. I think EBS volumes have a max size of 1TB. Which would be the approach if I need a filesystem bigger than 1TB? You are correct that the maximum EBS volume size is 1TB. We have an S3 object store in development (beta-ish, though some are already using it) that will replace the primary EBS-based storage as the default cloud galaxy object store using (free) instance ephemeral storage for the lifespan of a cluster, having all datasets persisted to S3 for the long term. This is on my roadmap to do this year, if the time-frame is useful. 3) Is possible to customize compute nodes with extra packages or config files? I suppose once the compute nodes are up and running I could ssh to them and do any modification but if the auto-scaling feature launch new compute nodes those new lauched nodes would not have my custom modifications. Is possible to do modifications that keep persistent even for new launched compute nodes? Sure, you can do this using a worker post start script configured for your cluster. See 'worker_post_start_script_url' at https://wiki.galaxyproject.org/CloudMan/UserData. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Uploading files
How large are the files you're attempting to upload? Another method for uploading with more reliability than web browsers would be to use FTP. See the documentation here for more details: https://wiki.galaxyproject.org/FTPUpload -Dannon On Tue, Jul 8, 2014 at 9:45 AM, Matthew Birnie matthew.bir...@bristol.ac.uk wrote: Hi, I am having trouble uploading files. I have been attempting to upload four files since noon (GMT) yesterday however the problem shows that the files are still uploading. I have cancelled the operation a couple of times hours after starting the upload to try again but still nothing is happening. Is there an issue at the moment with uploading files? Kind regards, Matthew Birnie -- matthew.bir...@bristol.ac.uk Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology School of Clinical Sciences University of Bristol Dorothy Hodgkin Building Whitson Street Bristol BS1 3NY (T) 0117 331 3124 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reset history dataset ?
No, since the integer X relates the file on disk to the Dataset object in the database. Technically, you could probably pull it off if you wanted to perform a bunch of database surgery, but I'd really not recommend it. -Dannon On Fri, Jul 4, 2014 at 3:43 AM, Pat-74100 leonardsqual...@hotmail.com wrote: Dear Galaxy developers. Running tools produce dataset_x.dat files in /database/files/ Looking this link https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets , I know we can purge and delete datasets . But new analysis produce dataset_(x+1). Is it possible to reset the dataset name ? that is restart from dataset_1.dat ? Thanks. Pat ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How does Galaxy differentiate users who have not logged on?
Jan is correct, this is what Galaxy does. -Dannon On Wed, Jun 25, 2014 at 6:29 AM, Jan Kanis jan.c...@jankanis.nl wrote: Probably the same way by which it keeps track of you when you are logged in: setting a cookie in the browser. I didn't verify this, but that is how basically all web services do it. If you clear the galaxy cookies I expect you will end up in a new empty workspace. On 25 June 2014 01:18, Melissa Cline cl...@soe.ucsc.edu wrote: Hi folks, Quick question. When two different users use the same Galaxy instance without logging in, how does Galaxy keep their identities straight, such that when they come back to their computers the next day, they see only their own workspace and not the other user's workspace? Thanks! Melissa ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How Galaxy prevents security attacks?
Hi Neil, Galaxy definitely takes this sort of thing very seriously. I'll take a look at the possible XSS locations identified in the report and verify whether or not they're actually vulnerable. For Denial of Service attacks, I'd suggest that this should be handled by the upstream proxy. You should *always* change id_secret in your universe_wsgi.ini, but it wouldn't be affecting your XSS tests. On Wed, Jun 18, 2014 at 8:48 AM, neil.burd...@csiro.au wrote: Hi, we'd like to host a version of Galaxy, but our security team have identified some potential areas that could be subjected to attack. I was wondering if Galaxy had mechanism in place to avoid the following issues: *Cross site scripting* *Description* Cross site scripting (also referred to as XSS) is a vulnerability that allows an attacker to send malicious code (usually in the form of Javascript) to another user. Because a browser cannot know if the script should be trusted or not, it will execute the script in the user context allowing the attacker to access any cookies or session tokens retained by the browser *Impact* Malicious users may inject JavaScript, VBScript, ActiveX, HTML or Flash into a vulnerable application to fool a user in order to gather data from them. An attacker can steal the session cookie and take over the account, impersonating the user. It is also possible to modify the content of the page presented to the user Affected URLS and parameters: · */capaibl/visualization/list * o update_time param · */capaibl/history/delete_current* o *purge * · */capaibl/history/list* o *F-deleted* o *F-name* · /*capaibl/user/edit_address* o*Address_id* o*User_id* · */capaibl/edit_info* o*Username* o*User_id* · *Capaibl/user/logout* o*Referrer* · */capaibl/user/manage_user_info* o*Change_password_button* o*Cntrller* o*Current* o*Email* o*Id* o*Message* o*Status* o*Username* o*User_id* · */capaibl/user/reset_password* o*Message* · */caibl/user/set_default_permissions* o*cntrller* *Denial of Service* *Description of attack* During security testing we used two different types of crawlers and both caused the system to crash. Without access to the backend it is hard to document the reason, however, an educated guess would be that there is limited memory available to sessions. When crawlers ask for multiple sessions, this could cause the webserver to allocate all its memory and crash. *Attack scenario* 1. Open burpsuite and start the proxy function 2. Open a browser and set burpsuite as the proxy 3. Navigate to the milxcloud homepage 4. Turn on the spider function within burpsuite The website will crash within seconds. There is an entry in universe_wsgi.ini # Galaxy encodes various internal values when these values will be output in # some format (for example, in a URL or cookie). You should set a key to be # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. #id_secret = USING THE DEFAULT IS NOT SECURE! Would this help address the XSS issue? Thanks for any information Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How Galaxy prevents security attacks?
One more detail I need -- which version of galaxy was your test suite run against? On Wed, Jun 18, 2014 at 8:59 AM, neil.burd...@csiro.au wrote: Thanks Dannon, The team gave this example (regarding XSS), Hope it helps Example: open firefox, log into galaxy and paste the following URL: 152.83.54.10/capaibl/visualization/list?async=falsef-free-text-search=ef-sharing=Allf-tags=Allf-title=Allpage=1show_item_checkboxes=falsesort=-update_time_/scriptscriptalert(you have been powned, right now an attacker would be stealing your cookie information)/scriptimg src=http://i.imgur.com/2ZTC4gh.jpg / Neil *From:* Dannon Baker [mailto:dannon.ba...@gmail.com] *Sent:* Wednesday, 18 June 2014 10:55 PM *To:* Burdett, Neil (CCI, Herston - RBWH) *Cc:* Galaxy Dev *Subject:* Re: [galaxy-dev] How Galaxy prevents security attacks? Hi Neil, Galaxy definitely takes this sort of thing very seriously. I'll take a look at the possible XSS locations identified in the report and verify whether or not they're actually vulnerable. For Denial of Service attacks, I'd suggest that this should be handled by the upstream proxy. You should *always* change id_secret in your universe_wsgi.ini, but it wouldn't be affecting your XSS tests. On Wed, Jun 18, 2014 at 8:48 AM, neil.burd...@csiro.au wrote: Hi, we'd like to host a version of Galaxy, but our security team have identified some potential areas that could be subjected to attack. I was wondering if Galaxy had mechanism in place to avoid the following issues: *Cross site scripting* *Description* Cross site scripting (also referred to as XSS) is a vulnerability that allows an attacker to send malicious code (usually in the form of Javascript) to another user. Because a browser cannot know if the script should be trusted or not, it will execute the script in the user context allowing the attacker to access any cookies or session tokens retained by the browser *Impact* Malicious users may inject JavaScript, VBScript, ActiveX, HTML or Flash into a vulnerable application to fool a user in order to gather data from them. An attacker can steal the session cookie and take over the account, impersonating the user. It is also possible to modify the content of the page presented to the user Affected URLS and parameters: · */capaibl/visualization/list * o update_time param · */capaibl/history/delete_current* o *purge * · */capaibl/history/list* o *F-deleted* o *F-name* · /*capaibl/user/edit_address* o*Address_id* o*User_id* · */capaibl/edit_info* o*Username* o*User_id* · *Capaibl/user/logout* o*Referrer* · */capaibl/user/manage_user_info* o*Change_password_button* o*Cntrller* o*Current* o*Email* o*Id* o*Message* o*Status* o*Username* o*User_id* · */capaibl/user/reset_password* o*Message* · */caibl/user/set_default_permissions* o*cntrller* *Denial of Service* *Description of attack* During security testing we used two different types of crawlers and both caused the system to crash. Without access to the backend it is hard to document the reason, however, an educated guess would be that there is limited memory available to sessions. When crawlers ask for multiple sessions, this could cause the webserver to allocate all its memory and crash. *Attack scenario* 1. Open burpsuite and start the proxy function 2. Open a browser and set burpsuite as the proxy 3. Navigate to the milxcloud homepage 4. Turn on the spider function within burpsuite The website will crash within seconds. There is an entry in universe_wsgi.ini # Galaxy encodes various internal values when these values will be output in # some format (for example, in a URL or cookie). You should set a key to be # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. #id_secret = USING THE DEFAULT IS NOT SECURE! Would this help address the XSS issue? Thanks for any information Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified
Re: [galaxy-dev] galaxy-dev Digest, Vol 96, Issue 14
This is a new one for me. What configuration are you using for both your
'database_connection', and the 'amqp_internal_connection' in your
universe_wsgi.ini?
On Fri, Jun 13, 2014 at 12:29 AM, xlwang xlwang_0...@163.com wrote:
Hello,
when i run my galaxy instance type:
$ sh run.sh
I get some error like this:
Traceback (most recent call last):
File /export/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
38, in app_factory
from galaxy.app import UniverseApplication
File /export/galaxy-dist/lib/galaxy/app.py, line 21, in module
from galaxy.queue_worker import GalaxyQueueWorker
File /export/galaxy-dist/lib/galaxy/queue_worker.py, line 10, in
module
import galaxy.queues
File /export/galaxy-dist/lib/galaxy/queues.py, line 17, in module
from kombu import Exchange, Queue
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/__init__.py, line
67, in __getattr__
module = __import__(object_origins[name], None, None, [name])
File /export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/entity.py,
line 10, in module
from .abstract import MaybeChannelBound
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/abstract.py, line
12, in module
from .connection import maybe_channel
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/connection.py, line
24, in module
from kombu import exceptions
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/exceptions.py, line
12, in module
from amqp import ChannelError, ConnectionError, ResourceError
File /export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/__init__.py,
line 32, in module
from .basic_message import Message # noqa
File
/export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/basic_message.py, line
19, in module
from .serialization import GenericContent
File
/export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/serialization.py, line
33, in module
from .five import int_types, long_t, string, string_t, items
File /export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/five.py, line
171, in module
librt = ctypes.CDLL('librt.so.1', use_errno=True)
TypeError: __init__() got an unexpected keyword argument 'use_errno'
I have no idea why this happend. How can I fix it?
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Re: [galaxy-dev] Galaxy updated botched?
Hey Hans (and anyone else using MySQL), Just to clarify -- MySQL doesn't have this (particular) error by default and as long as your server default table type has not and does not change you should be fine. I've just successfully tested MySQL using MyISAM all the way to the current tip revision and you should be able to upgrade safely when the time comes. -Dannon On Thu, Jun 12, 2014 at 2:01 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 06/12/2014 12:06 AM, John Chilton wrote: If anyone out there has tired using Galaxy with strictly MyISAM tables and found it untenable - by all means please chime in. Well, due to several reasons we are (still) using MySQL (version: 5.1.69) with only MyISAM tables. We have been running into troubles but they were never related to running MyISAM. However, I haven't done the latest Galaxy code upgrade, hence we are still on database version '118'. So, I am curious to see what will happen when I do the next upgrade (after GCC). Also, on my list of things to do for this year is actually changing all our Galaxy servers from MySQL to PostgreSQL. With my current workload, I doubt I will manage to do this and have to postpone this 'adventure' to next year. Regards, Hans-Rudolf ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy updated botched?
Hey Iyad, I just want to second (and add slightly) to what John said here. I had also failed to reproduce this locally, but that makes perfect sense now -- I'm glad you figured it out, and thanks for looking into this so closely and reporting back. Like John said, I wouldn't modify the migrations to force or assume a particular engine, but if you wanted to make a contribution to the code base it would probably be worth improving the detection and reporting of this particular error condition to help anyone else who might run into the issue -- if you wanted to take a stab at that. On Wed, Jun 11, 2014 at 10:08 AM, John Chilton jmchil...@gmail.com wrote: Spent a couple hours yesterday trying to track down this - I was not getting anywhere though and I see why now. Well this definitely an unfortunate situation - but I think documentation improvements are the right fix not enforcing the engine type in sqlalchemy migrations. For one, I don't think we can assume a particular engine type because different deployers may already going to have both kinds out there right? I think it would be better to update the wiki to encourage InnoDB for all new installations and warn this can happen for MySQL upgrades. Is this okay? Sorry about this. -John On Wed, Jun 11, 2014 at 8:48 AM, Kandalaft, Iyad iyad.kandal...@agr.gc.ca wrote: This is a follow up for those that are interested with regards to my failed schema upgrade. I believe I have determined why all the tables are set to use the MyISAM engine. When I initialized galaxy on our enterprise servers, they were running a dated version of CentOS. Hence, the OS defaults to a dated MySQL version. MySQL only switched to using InnoDB (over MyISAM) as the default engine in version 5.5. If I’m not mistaken, I initialized galaxy in MySQL 5.1 without changing the default engine to InnoDB (big mistake). Due to my ignorance, I will now have to try to compare v118 of our database with a new install of galaxy running schema v118. Then, I will try “migrating” to the true schema state without destroying the data. I do feel that I should still modify the galaxy schema to set the MySQL engine to InnoDB to thwart problems like this for other unsuspecting users. If anyone can point me at some documentation about how Galaxy schema changes should occur in this case, that would be great. As per my previous comment, I’m not certain whether I would edit all schema versions to ensure table definitions include the mysql_engine=InnoDB attribute or whether using a DDL event in SQLAlchemy. I suspect that setting this option globally would mean that future developers don’t need to remember to define mysql_engine on every new table. Iyad Kandalaft Microbial Biodiversity Bioinformatics Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada 960 Carling Ave.| 960 Ave. Carling Ottawa, ON| Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel iyad.kandal...@agr.gc.ca Telephone | Téléphone 613-759-1228 Facsimile | Télécopieur 613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600 Government of Canada | Gouvernement du Canada From: Kandalaft, Iyad Sent: Tuesday, June 10, 2014 1:39 PM To: 'galaxy-...@bx.psu.edu' Subject: Re: Galaxy updated botched? Hi Everyone, This is follow-up information/questions to the issue I ran into with the galaxy June 2nd, 2014 update. I hope to receive feedback on how to proceed. Background: - Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end - When updating galaxy to the june 2nd release, the v120 DB schema has referential integrity constraints, which produced errors during the upgrade. - Completed two galaxy updates in the past 4 months without encountering this before (schema changes included) Discussion: In the past, referential integrity in the DB schema was never an issue. I checked backups and the current database to find that the database tables are using the MyISAM engine. MyISAM = no referential integrity support, no transactions. I reviewed galaxy’s SQLAlchemy templates and determined that mysql_engine='InnoDB' isn’t set on tables. This explains why all tables were created with the MyISAM engine. If the mysql_engine is not innodb, SQL Alchemy is supposed to drop any referential integrity constraints defined in the schema. What I don’t understand is why SQL Alchemy is no longer ignoring the referential integrity constraints. Going forward, can anyone propose how I can salvage the database or continue ignoring referential integrity for now? Assuming that my limited understanding of SQLAlchemy holds water, I was looking at fixing the galaxy code base but I need some clarification on the DB schema versioning. Do I edit schema v1 and add the appropriate table
Re: [galaxy-dev] Missing navigation pane
Hey Stephen, Can you look in the server logs to see if there are any errors being reported? Or if there are any javascript errors in the browser window? You may also want to try clearing your browser cache. -Dannon On Tue, Jun 10, 2014 at 1:54 AM, Stephen E sedwards...@hotmail.com wrote: I installed a local instance of galaxy approximately a month ago (build 2014.04.14). I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem. I ran hg pull and then hg update latest_2014.06.02. I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade). When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it. How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending /admin to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports crashing with the latest stable release
I'm having trouble reproducing this. The base grid object that's used by the SpecifiedDateListGrid does have that info_text field -- it's almost as if you're somehow using an outdated grid module, while the rendering template is current. It's a bit brute force, but can you try (from the base of your galaxy directory) something like: find . -name '*.pyc' -delete and restart your reports app? On Wed, Jun 4, 2014 at 5:10 AM, bjoern.gruen...@googlemail.com bjoern.gruen...@gmail.com wrote: Hi, I encountered the following bug during my testing of the latest stable release: Error - type 'exceptions.AttributeError': 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 177 in specified_date_handler return self.specified_date_list_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 296 in __call__ message = message, File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1184 in fill_template def fill_template(self, filename, **kwargs): File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1199 in fill_template_mako template_lookup = template_lookup or self.webapp.mako_template_lookup File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 193 in render_get_grid_config 'info_text' : grid.info_text, AttributeError: 'SpecifiedDateListGrid' object has no attribute 'info_text' Trello card is here: https://trello.com/c/EqQCAcIe Thanks, Bjoern ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Bioblend dependency error
Hey Nikos,
I think you're seeing the same issue from this trello card here:
https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
That should re-fetch galaxy's eggs and you should be up and running again.
On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi all,
after the latest galaxy update I've experienced the following error while
trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in t
he egg distribution.
galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util
/pastescript/serve.py, line 1055, in invoke
exit_code = runner.run(args)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('bioblend')
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 409, in require
return c[req.project_name].require()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 237, in require
dists = self.resolve()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('mock'))
First I got and error about the python module 'requests' missing, fixed it
using 'pip install', and then got the error above.
Regards,
Nikos
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___
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Re: [galaxy-dev] Bioblend dependency error
Most of them include at least at little documentation in the code, and the
egg ones are documented here:
https://wiki.galaxyproject.org/Admin/Config/Eggs
There's not (that I know of or could find) a single wiki page documenting
all scripts, but that's not a bad idea.
On Wed, Jun 4, 2014 at 9:32 AM, Evan Bollig boll0...@umn.edu wrote:
Dannon,
Do you guys have a web page that documents all of the script/ utilities? I
know most of my deployment and upgrade problems have been resolved by
various scripts in there, but I have no idea what's available until I turn
to this mailing list.
-E
On Wednesday, June 4, 2014, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Nikos,
I think you're seeing the same issue from this trello card here:
https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
That should re-fetch galaxy's eggs and you should be up and running again.
On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi all,
after the latest galaxy update I've experienced the following error
while trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
depends on something which is missing, this is almost certainly a bug in t
he egg distribution.
galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency bioblend requires
mock
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File /steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util
/pastescript/serve.py, line 1055, in invoke
exit_code = runner.run(args)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('bioblend')
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 409, in require
return c[req.project_name].require()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 237, in require
dists = self.resolve()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('mock'))
First I got and error about the python module 'requests' missing, fixed
it using 'pip install', and then got the error above.
Regards,
Nikos
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Re: [galaxy-dev] Bioblend dependency error
So the problem now is that you have conflicting eggs on your system path
that are getting loaded prior to the galaxy supplied eggs. Galaxy manages
its own dependencies, and not relying on those installed via pip/etc.
The simplest, most fool-proof solution here is to use a virtualenv and
start galaxy in a clean environment. See the virtualenv bit here:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
Basically, you're going to want to:
pip install virtualenv
virtualenv env_galaxy_clean
source env_galaxy_clean/bin/activate
sh run.sh (or otherwise launch galaxy from within this new environment)
On Wed, Jun 4, 2014 at 10:25 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Dannon,
`python scripts/fetch_eggs.py` failed with errors about more packages
(pycrypto, poster).
After installing them and running the 'fetch_eggs' script successfully I'm
getting this error upon starting the server:
galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency bioblend requires
simplejson
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1049, in run
invoke(command, command_name, options, args[1:])
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 1055, in invoke
exit_code = runner.run(args)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 220, in run
result = self.command()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py,
line 643, in command
app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 375, in loadobj
return context.create()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 813, in create
return self.object_type.invoke(self)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 249, in invoke
return fix_call(context.object, context.global_conf,
**context.local_conf)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py,
line 97, in fix_call
val = callable(*args, **kw)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('bioblend')
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 409, in require
return c[req.project_name].require()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 237, in require
dists = self.resolve()
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2
(/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg),
Requirement.parse('simplejson'))
Simplejson is installed in the system and the library folder is in the
galaxy user's PYTHONPATH.
On 4 June 2014 15:32, Evan Bollig boll0...@umn.edu wrote:
Dannon,
Do you guys have a web page that documents all of the script/ utilities?
I know most of my deployment and upgrade problems have been resolved by
various scripts in there, but I have no idea what's available until I turn
to this mailing list.
-E
On Wednesday, June 4, 2014, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Nikos,
I think you're seeing the same issue from this trello card here:
https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail
Can you run `python scripts/fetch_eggs.py` from your galaxy directory?
That should re-fetch galaxy's eggs and you should be up and running again.
On Wed, Jun 4, 2014 at 9
Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host
Hey Eric, It looks like you have connection info for both tcp/ip connections and unix sockets in the connection strings. If you're logging in using psql -h wigserv5.cshl.edu snip, then you only want the tcp/ip connection info. Drop the ?host=tmp off the third option you listed and I think you'll be up and running, so: postgresql://glxeric:xx...@wigserv5.cshl.edu:5432/glxeric -Dannon On Sat, May 24, 2014 at 1:49 AM, Paniagua, Eric epani...@cshl.edu wrote: Dear Galaxy Developers, I've been banging my head against this one for a few days now. I have two Galaxy instances. One resides on a server called genomics, which also hosts the corresponding PostgreSQL installation. The second also resides on genomics, but its database is hosted on wigserv5. Based on the tests I just ran and code I just read, sqlalchemy (not Galaxy) is ignoring the hostname/port part of the database_connection string. For reference, the connection strings I've tried are: postgresql://glxeric:X@/glxeric?host=/tmp postgresql://glxeric:xx...@wigserv5.cshl.edu/glxeric?host=/tmp postgresql://glxeric:xx...@wigserv5.cshl.edu:5432/glxeric?host=/tmp postgresql://glxeric:X@adgdgdfdflkhjfdhfkl/glxeric?host=/tmp All of these appear to result in Galaxy connecting to the PostgreSQL installation on genomics, as determined by Galaxy schema version discrepancies and other constraints. With each connection string, Galaxy starts up normally. I force database activity by browsing saved histories. It works every time. By all appearances, the second Galaxy instance is using the PostgreSQL database hosted on genomics, not on wigserv5. All databases and roles exist, and the databases are populated. When I comment out the database_connection line in universe_wsgi.ini, I get errors arising from the later configuration of PostgreSQL-specific Galaxy options, as expected. I can connect to the database server on wigserv5 using psql -h wigserv5.cshl.edu -d glxeric -U glxeric from the server genomics. Have you ever observed this behavior from Galaxy or sqlalchemy? Thanks, Eric ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Changes in admin menu - Upload files
Cross-post from biostar, answered there: https://biostar.usegalaxy.org/p/7747/#7760 On Mon, May 26, 2014 at 6:47 AM, Julien Daligault daliga...@ijm.univ-paris-diderot.fr wrote: Hi, I manage a galaxy instance on a local server and I want that users use only the filesystem paths to create a link to their data by the Admin Menu. Where can I find the source file to modify the web page in order to appear directly this option in first in the drop-down menu ? It will avoid to load directly big data on our computing machine. Thanks Julien -- Julien Daligault Plateforme Génomique-Transcriptomique (583B) INSTITUT JACQUES MONOD CNRS-Université Paris Diderot Bât. Buffon - 15 rue Hélène Brion 75205 Paris Cedex 13 - France tel : +33 1 57 27 81 31 daliga...@ijm.univ-paris-diderot.fr ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host
On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric epani...@cshl.edu wrote: Thanks for pointing that out! I missed it. I am now connecting to the remote database. I ran sh manage_db.sh upgrade and it upgraded from schema 114 to 118 without error messages. I then ran sh ./scripts/migrate_tools/0010_tools.sh install_dependencies and received the following error: line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' I fixed this by adding the appropriate entries to tool_data_table_conf.xml. I then reran the migrate_tools command successfully. However, now my history_dataset_association table in the database was blown away at some point. The table is now completely empty. Have you ever seen this before? I have not seen the tool migration issue before, but it seems harmless. The fact that your history_dataset_association table is empty is concerning if there was ever anything in it. Can you verify that there are datasets in the same database that *should* be associated to a history? It sounds like this galaxy instance has been used with different databases, and my hope is that the wires are crossed up here and there actually should not be any. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host
Since the database has lost consistency, I'd really try a fresh pg_dump / import if that's possible. If there's an error this time around, note it and send it on over and we can figure out where to go from there. On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric epani...@cshl.edu wrote: The dataset table is populated. I looked at the SQL dump file I used to copy the database, and it has create table and copy into statements for history_dataset_association, but it looks like there may have been an error while executing them. Trying to figure out how to get my data in... From: Dannon Baker [dannon.ba...@gmail.com] Sent: Tuesday, May 27, 2014 11:43 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem using Galaxy with a PostgreSQL database on a remote host On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric epani...@cshl.edu mailto:epani...@cshl.edu wrote: Thanks for pointing that out! I missed it. I am now connecting to the remote database. I ran sh manage_db.sh upgrade and it upgraded from schema 114 to 118 without error messages. I then ran sh ./scripts/migrate_tools/0010_tools.sh install_dependencies and received the following error: line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes' I fixed this by adding the appropriate entries to tool_data_table_conf.xml. I then reran the migrate_tools command successfully. However, now my history_dataset_association table in the database was blown away at some point. The table is now completely empty. Have you ever seen this before? I have not seen the tool migration issue before, but it seems harmless. The fact that your history_dataset_association table is empty is concerning if there was ever anything in it. Can you verify that there are datasets in the same database that *should* be associated to a history? It sounds like this galaxy instance has been used with different databases, and my hope is that the wires are crossed up here and there actually should not be any. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Repository installation on multiple servers
On Fri, May 23, 2014 at 9:07 AM, Greg Von Kuster g...@bx.psu.edu wrote: I'm not quite sure whether this baseline implementation will handle comunication between Galaxy web front-ends like you have (and like we have for our public Galaxy instances). Yep, it sure does. There's still a little bit of work to do on it, but it'll be in the release. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Display problem with partial loading of tabular data
Hey Peter, By default, galaxy attempts to ship 50kb chunks of tabular data. It's a good idea to probably support a minimum number of 'lines' to ship as well, for text-based data -- I'll add a Trello card for this and will plan to work on it soon. That, and there should be an indicator along the lines of your entire dataset has not loaded yet, click here or scroll to load more. -Dannon On Fri, May 23, 2014 at 9:38 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hello all, Large tabular data files in Galaxy are shown with auto loading, meaning more data is loaded as you scroll down the page. (As an aside, this can cause confusion, e.g. using CTRL+F to search in the web browser would miss not-yet-loaded content.) I've noticed with many BLAST tabular files with 25 columns (often quite wide with sequences in columns 21 and 22) that Galaxy does not load enough to fill the page. e.g. Only 14 rows are shown. I order to get the rest to load (on Firefox or Safari at least), I must scroll *right* to trigger more to load. This is a problem as at first glance the interface implies that the fill dataset is loaded - there is no vertical scroll bar or other visual indicator :( Have I explained this clearly enough? Would some images help? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] download workflow error
Yep, your guess looks correct. We enforced creation of a public username at registration a long while back, but it looks like the API doesn't do the same enforcement (and neither does the web interface, anymore -- d'oh). I'll get a bugfix out shortly. On Thu, May 22, 2014 at 11:12 AM, Evan Bollig boll0...@umn.edu wrote: I have a fresh instance of galaxy-dist#stable. I create users and upload a workflow via the internal python api, and then I attempt to edit and download the workflow from the workflow editor tab. I click the direct download link and get the attached exception. I found that the exception is avoided if I instead share/export the workflow and then create a public username when prompted. When I go back and use the direct download link again, it works. Not sure if they're directly connected, but something in the share/export seems to band-aid the other. Presumably the 'None' should be the public username. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] warning text
Hi Evan, It looks like that message might actually list the two versions backwards. I'll check into it and, if that's the case, get a fix out shortly. In any event, you should be able to edit and re-save the workflow as indicated to keep moving forward. -Dannon On Tue, May 20, 2014 at 3:02 PM, Evan Bollig boll0...@umn.edu wrote: Galaxy Team: I'm confused. This warning appears when I import an old workflow into the latest version of galaxy-dist#stable. As I interpret the first message, I see galaxy has fastqc 0.3 installed, but the workflow was written with fastqc 0.52 and will need to be updated to use the version 0.3 tool. This must be wrong, no? Perhaps I'm installing tools from the wrong toolshed, but I would expect the main galaxy toolshed to have *newer*, not older versions of tools available as months progress. My guess is that your verbose message needs to be polished. If you look at the second attached screenshot, I believe that confirms that I have fastqc 0.52 installed. In that case, you probably need to tell users, fastqc: using version '0.52' instead of version '0.3' indicated in this workflow. (note that the version strings are swapped). Perhaps add a bit more to the message to avoid confusion. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105
Ok, great, glad you're up and running! I'll scratch this one off the list of things to think about. On Mon, May 19, 2014 at 4:00 PM, Evan Bollig boll0...@umn.edu wrote: Hey Dannon, I managed to resolve this on my own. The postgres version is 9.1, and I'm on Ubuntu 12.04. The instance is an OpenStack VM. It turned out that the dir contained files that were outdated from a previous version of galaxy-dist. After I realized that they were part of hgignore, I ran hg clean --all to make sure I was working with a fresh install. Cheers, -E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 e...@msi.umn.edu boll0...@umn.edu On Fri, May 16, 2014 at 2:39 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Fri, May 16, 2014 at 3:33 PM, Evan Bollig boll0...@umn.edu wrote: InvalidVersionError: 103 is not 105 This would indicate to me that migration script 104 failed. My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails? It is, in a sense, hence all the other migration steps. Can you provide more details about your configuration? Postgres version, whether you're using a virtualenv (or not), or anything else you think seems relevant? -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Fwd: InvalidVersionError: 103 is not 105
On Fri, May 16, 2014 at 3:33 PM, Evan Bollig boll0...@umn.edu wrote: InvalidVersionError: 103 is not 105 This would indicate to me that migration script 104 failed. My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails? It is, in a sense, hence all the other migration steps. Can you provide more details about your configuration? Postgres version, whether you're using a virtualenv (or not), or anything else you think seems relevant? -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here
Hey Peter,
Just looking at the travis job, it looks like there's not a fetch_eggs step
at the start, but rather that it's fetching as they're require()'d. Is
that correct? In any event, I'm changing the order of those requires
in 13302:92519a9bfa32, which may resolve your issue. They work fine like
that in production with eggs fetched ahead of time, but I could see how
that'd cause the failure you're seeing.
-Dannon
On Mon, May 5, 2014 at 9:14 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hi all,
Recently my TravisCI tests have started failing during the tool
functional tests due to what looks like a missing dependency:
e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/2682
...
galaxy.eggs DEBUG 2014-05-05 11:26:47,387 Fetched
http://eggs.galaxyproject.org/boto/boto-2.27.0-py2.7.egg
galaxy.eggs DEBUG 2014-05-05 11:26:47,753 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
Traceback (most recent call last):
File ./scripts/functional_tests.py, line 601, in module
sys.exit( main() )
File ./scripts/functional_tests.py, line 417, in main
use_translogger=False, static_enabled=STATIC_ENABLED )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 20, in module
eggs.require('pyyaml')
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py,
line 412, in require
return pkg_resources.working_set.require( req_str )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py,
line 666, in require
needed = self.resolve(parse_requirements(requirements))
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py,
line 565, in resolve
raise DistributionNotFound(req) # XXX put more info here
pkg_resources.DistributionNotFound: pyyaml
Is there a missing egg declaration for pyyaml?
I found this commit about a PyYAML 3.10 egg., perhaps linked?
https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb0ae5e117ca33e0ad231535186d6d
Thanks,
Peter
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Re: [galaxy-dev] specify file_path for each Galaxy registered users
Hey Weiyan, You can't (currently) specify disk destinations per user, but you can certainly use multiple disks in a pool. For one example, see the sample object store configuration here (and also in your galaxy distribution): https://bitbucket.org/galaxy/galaxy-central/src/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e/object_store_conf.xml.sample?at=default There isn't currently formal documentation for this (that I could find just now), but I'm happy to help if you run into any issues. -Dannon On Sat, May 3, 2014 at 11:32 PM, Weiyan Shen shenw...@gmail.com wrote: Galaxy developers: We can set the *file_path *in universe_wsgi.ini to specify the saved Galaxy results.But whether it is possible for us to specify *file_path*for each Galaxy registered users,for which multi-hard disks can be used effectively in some ways? Thank you very much for any help. Regards,Weiyan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] File upload error
Are you using usegalaxy.org? This generally indicates a temporary error with one of our cluster node (if using usegalaxy.org), or a misconfiguration of the job management system if you're seeing this on a local cluster. If you're using usegalaxy.org I'd recommend simply retrying the upload. -Dannon On Sat, May 3, 2014 at 4:21 PM, Heller Gerwin gerwin.hel...@meduniwien.ac.at wrote: Hello! I tried to upload some file to Galaxy but received th error Job output not returned from cluster. I got it for the first time, file upload always worked in the past. What can I do? Thanks for help, Gerwin -- Gerwin Heller, Ph.D. Medical University of Vienna Department of Medicine I Division of Oncology Währinger Gürtel 18-20 A-1090 Vienna, Austria Phone: +43 1 40400 4433 Fax: +43 1 40400 4451 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here
Can you add a `python scripts/fetch_eggs.py` to your travis config just
after the stop-daemon? That should parse eggs.ini and fetch all of the
eggs.
On Mon, May 5, 2014 at 9:51 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Mon, May 5, 2014 at 2:30 PM, Dannon Baker dannon.ba...@gmail.com
wrote:
Hey Peter,
Just looking at the travis job, it looks like there's not a fetch_eggs
step
at the start, but rather that it's fetching as they're require()'d. Is
that
correct?
Yes, https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml
does not (currently) attempt to fetch any eggs explicitly - it lets the
different bits of Galaxy do this on demand.
Is there a simple command line instruction to tell Galaxy to fetch
all the eggs it might want?
In any event, I'm changing the order of those requires in
13302:92519a9bfa32, which may resolve your issue. They work fine like
that
in production with eggs fetched ahead of time, but I could see how that'd
cause the failure you're seeing.
https://bitbucket.org/galaxy/galaxy-central/commits/92519a9bfa32a42ce47a63fdb72c8e2d717ec52e
It looks like John has his Galaxy mirror automatically updates (or he
did a push just now), so I could ask TravisCI to retest immediately.
[In earlier testing GitHub was faster than BitBucket for fetching Galaxy]:
https://github.com/jmchilton/galaxy-central/commit/9e72c14ef176e494a611bee6441477a05fb8e677
Unfortunately, no real change:
...
functional_tests.py INFO 2014-05-05 13:44:46,611 Embedded Universe
application started
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,684 Enabling
'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,685 Enabling
'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,758 Enabling
'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,762 Enabling
'library' controller, class: Library
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,765 Enabling
'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2014-05-05 13:44:46,773 Enabling
'tool_runner' controller, class: ToolRunner
galaxy.eggs DEBUG 2014-05-05 13:44:46,958 Fetched
http://eggs.galaxyproject.org/SVGFig/SVGFig-1.1.6-py2.7.egg
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,116 Enabling
'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,189 Enabling
'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,190 Enabling
'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,202 Enabling
'data_admin' controller, class: DataAdmin
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,246 Enabling
'user' controller, class: User
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,256 Enabling
'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2014-05-05 13:44:47,260 Enabling
'ucsc_proxy' controller, class: UCSCProxy
Traceback (most recent call last):
File ./scripts/functional_tests.py, line 601, in module
sys.exit( main() )
File ./scripts/functional_tests.py, line 417, in main
use_translogger=False, static_enabled=STATIC_ENABLED )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/buildapp.py,
line 49, in app_factory
webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/web/framework/__init__.py,
line 441, in add_ui_controllers
module = import_module( module_name )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/util/backports/importlib/__init__.py,
line 37, in import_module
__import__(name)
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py,
line 18, in module
eggs.require('pyyaml')
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py,
line 412, in require
return pkg_resources.working_set.require( req_str )
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py,
line 666, in require
needed = self.resolve(parse_requirements(requirements))
File
/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/pkg_resources.py,
line 565, in resolve
raise DistributionNotFound(req) # XXX put more info here
pkg_resources.DistributionNotFound: pyyaml
galaxy.jobs.handler INFO 2014-05-05 13:44:47,295 sending stop signal
to worker thread
galaxy.jobs.handler INFO 2014-05-05 13:44:47,296 job handler queue stopped
...
Peter
Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here
On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.c...@googlemail.comwrote: However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)? Yep, I've adjusted that now and my guess is it'll work next time. Let me know if it doesn't, and thanks for finding the issue! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing pyyaml - raise DistributionNotFound(req) # XXX put more info here
If they're fetching as it runs the tests, you may not need to do it up front explicitly. It's worth noting, though, that this is how galaxy normally runs (checking for and fetching eggs up front -- except when using the --stop-daemon argument) under run.sh. On Mon, May 5, 2014 at 11:15 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, May 5, 2014 at 3:47 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Mon, May 5, 2014 at 10:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote: However, while it pre-fetched PyYAML-3.10-py2.7-linux-x86_64-ucs4.egg the old error persists. Is there a case-sensitivity issue here (PyYAML versus pyyaml)? Yep, I've adjusted that now and my guess is it'll work next time. Let me know if it doesn't, and thanks for finding the issue! Green light :) https://travis-ci.org/peterjc/pico_galaxy/builds/24456751 I'm checking if I actually did need the fetch eggs or not... Thank you, Peter (Apologies for previous blank email, slip of the mouse) ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy - Cloudman
Do you have Cloudman admin access on this instance?
The first thing I'd check would be http://your_instance/cloud to verify
that your instance has free disk space and to look for any errors in the
log. Then, check out the admin service list
(http://your_instance/cloud/admin)
to see if there are any service issues. Next to the SGE service, you
should see a 'qstat' link that'll show you the status of any jobs submitted
to the cluster. If you're not running any extra worker nodes, check this
page to verify that the master is set to run jobs.
If you look through this stuff and nothing looks obvious, feel free to ping
me off list and I can try to take a look with you.
-Dannon
On Fri, Apr 25, 2014 at 2:18 AM, Alessia Deglincerti
adeglin...@mail.rockefeller.edu wrote:
Hey Dannon,
I am using Galaxy (Cloudman) to analyze RNA seq data. I have a bunch of
datasets that I ran TopHat on. I am now trying to run Cufflinks etc. I used
the same data and workflow yesterday to run Cufflinks etc and that worked
fine. I used my own reference annotation (Homo sapiens hg38) that I
imported from UCSC but I wanted to compare to some older data I have and so
now I trying to run it on hg17. I also have some other datasets in the
queue. All my jobs are gray and have been waiting to ran for the past 24+
hours. I am seeing the error as I am waiting for my jobs to run, I get a
notification at the top of my queue/history saying that there was a problem
getting updates and to contact a site administrator if the problem persists
(I've seen the notification a few times) and when I click the details
link in the notification it prompts me with the details pasted below.
I am using all of the default options for my jobs and the same workflow
has been working fine for me in the past on the same datasets.
Thanks for any help you can give me!
Alessia
On Apr 24, 2014, at 10:24 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Alessia,
I'd love to help, but I need a little more context here. Where are you
seeing this error, what exactly are you doing when it appears, and can you
tell me a little bit more about the Galaxy configuration you're working
with?
-Dannon
On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Posting to the galaxy-...@bx.psu.edu mailing list.
https://wiki.galaxyproject.org/MailingLists
My instance of Galaxy seems to be stuck (same place since last night)
and I have received the error message several times now.
Pasting the error message below:
*Details*
user
username
adeglincer
quota_percent
68
total_disk_usage
184947273683
nice_total_disk_usage
172.2 GB
email
xxx
is_admin
false
tags_used
model_class
User
id
xxx
source
HDACollection(xxx)
xhr
readyState
4
responseText
{err_msg: Uncaught exception in exposed API method:, err_code: 0}
responseJSON
err_msg
Uncaught exception in exposed API method:
err_code
0
status
500
statusText
Internal Server Error
responseHeaders
Date
Thu, 24 Apr 2014 20:51:39 GMT
cache-control
max-age=0,no-cache,no-store
Server
nginx/1.4.7
Connection
keep-alive
Transfer-Encoding
chunked
Content-Type
application/json
options
data
parse
true
emulateHTTP
false
emulateJSON
false
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy/Cloudman Compute Nodes User
Hi Jim, /mnt/galaxy is shared via NFS with all cluster workers -- this (or a subdirectory) should work for you. -Dannon On Fri, Apr 25, 2014 at 10:56 AM, Jim McCusker jmccus...@5amsolutions.comwrote: Hi all, I need to add a .boto file to the user that galaxy jobs get exec'ed as on cloudman nodes. I thought it would copy over what the galaxy server has in its home directory, but that doesn't seem to happen. How can I get things like my .boto file to migrate over to new cloudman nodes when they are spun up? Thanks, Jim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] workflow_execute_parameters.py
Olivia, Is the parameter set to 'set at runtime' when you view the workflow in the editor? Could you send me the workflow json (just the http://127.0.0.1:8080/api/workflows/workflow_id/ bit)? -Dannon On Fri, Apr 25, 2014 at 5:26 AM, Olivia Doppelt-Azeroual olivia.dopp...@pasteur.fr wrote: Dear Dannon, Thank you for your answer, it works better now that I know the steps ID for my workflow. I have another question though. The second step of my WF uses a parameter input named prefix. I really need to specify it when I launch the WF using the API. When i display the WF using the url you gave me, the parameters prefix, is not there and when I use this in my command line, the specified Value is not read by Galaxy. python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27 http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e985db '10=hda=52ea4fd71e9f7c3f' 'param=export_sbw=prefix=test' Could you help me on that ? How do I give a value to a parameter if it does not appear in the WF description ?? Thanks in advance, -- Olivia Le 23/04/14 18:40, Dannon Baker a écrit : Hi Olivia! It's probably talking about the workflowstep object with identifier 8. If you request the description of this workflow via the API ( http://yourgalaxyinstance.org/api/workflows/the id of this workflow), you'll be given the exact step identifiers to use. In other words, unless this is the first workflow ever created on a brand new galaxy instance, your step ids will not be 0 and 1. -Dannon On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual olivia.dopp...@pasteur.fr wrote: Dear developpers, I'm trying to launch a small workflow using the api script workflow_execute_parameters.py I have 2 steps: the input data step and a second step which needs a parameter called prefix. The workflow is attached to this email. I get an error on the parameters inputs which asks me to specify information about an 8th step (which does not exist) Is there a test case available to use this script ? Please keep me informed on that. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman/Galaxy autoscaling
You can review the exact code here( see 'slow_job_turnover') : https://bitbucket.org/galaxy/cloudman/src/7b8f04895ad309e0168cb3de66446ae20f3d8b3e/cm/services/autoscale.py?at=default But, basically, load on any particular node isn't very useful for autoscaling in this context because most jobs cannot be split among multiple nodes. What we use is a heristic to determine churn and jobs waiting to run. Generally speaking, if you have jobs waiting to run for a bit, your cluster should scale. -Dannon On Fri, Apr 25, 2014 at 2:37 PM, Jim McCusker jmccus...@5amsolutions.comwrote: What are the exact conditions that will trigger autoscaling in a galaxy/cloudman instance? I'm seeing 100% utilization on the head node but no attempts by cloudman at spinning up new instances. What sort of state is supposed to trigger that? Thanks, Jim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy - Cloudman
Hey Alessia,
I'd love to help, but I need a little more context here. Where are you
seeing this error, what exactly are you doing when it appears, and can you
tell me a little bit more about the Galaxy configuration you're working
with?
-Dannon
On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Posting to the galaxy-...@bx.psu.edu mailing list.
https://wiki.galaxyproject.org/MailingLists
My instance of Galaxy seems to be stuck (same place since last night)
and I have received the error message several times now.
Pasting the error message below:
*Details*
user
username
adeglincer
quota_percent
68
total_disk_usage
184947273683
nice_total_disk_usage
172.2 GB
email
xxx
is_admin
false
tags_used
model_class
User
id
xxx
source
HDACollection(xxx)
xhr
readyState
4
responseText
{err_msg: Uncaught exception in exposed API method:, err_code: 0}
responseJSON
err_msg
Uncaught exception in exposed API method:
err_code
0
status
500
statusText
Internal Server Error
responseHeaders
Date
Thu, 24 Apr 2014 20:51:39 GMT
cache-control
max-age=0,no-cache,no-store
Server
nginx/1.4.7
Connection
keep-alive
Transfer-Encoding
chunked
Content-Type
application/json
options
data
parse
true
emulateHTTP
false
emulateJSON
false
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] purging deleted datasets
Hi Milad, That's just a warning, it should not cause any issues (I've just confirmed this locally on a sqlite instance). So you're sure you have histories with deleted datasets older than 0 days? The commands you have run will not remove datasets that haven't been deleted first by a user (usually through the history panel). -Dannon On Wed, Apr 23, 2014 at 9:21 AM, Milad Bastami mi.bast...@live.com wrote: Dear all, I have some unwanted datasets to remove but I need their main histories, so in galaxy I just deleted the unwanted datasets but not the histories. Then I tried to purge the deleted datasets with the following commands: *python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -6 -r * *python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -3 -r * and I saw the this error: */galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.* *Purged 0 datasetsFreed disk space: 0Elapsed time: 0.0748069286346* Unfortunately I can't understand the warning and why nothing was deleted. Any help would be most appreciated. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] workflow_execute_parameters.py
Hi Olivia! It's probably talking about the workflowstep object with identifier 8. If you request the description of this workflow via the API ( http://yourgalaxyinstance.org/api/workflows/the id of this workflow), you'll be given the exact step identifiers to use. In other words, unless this is the first workflow ever created on a brand new galaxy instance, your step ids will not be 0 and 1. -Dannon On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual olivia.dopp...@pasteur.fr wrote: Dear developpers, I'm trying to launch a small workflow using the api script workflow_execute_parameters.py I have 2 steps: the input data step and a second step which needs a parameter called prefix. The workflow is attached to this email. I get an error on the parameters inputs which asks me to specify information about an 8th step (which does not exist) Is there a test case available to use this script ? Please keep me informed on that. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id
Hey Pieter, sure. The sqlite database is in sqlite3 format, so you'll need to use 'sqlite3 database/universe.sqlite' to access it. The following should work: sqlite3 database/universe.sqlite '.dump migrate_tmp' temporary_backup.sql sqlite3 database/universe.sqlite 'drop table migrate_tmp;' And, once that's done, verify that everything works as expected and that whatever table is in temporary_backup.sql actually did get migrated. -Dannon On Tue, Apr 22, 2014 at 8:41 AM, Lukasse, Pieter pieter.luka...@wur.nlwrote: Hi Dannon, I’m facing the same problem now. Could you help me with the steps to delete the migrate_tmp table manually? I’m trying to use sqlite from command line but get the following error: Unable to open database universe.sqlite: file is encrypted or is not a database Thanks and regards, Pieter. *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Dannon Baker *Sent:* dinsdag 18 februari 2014 14:40 *To:* Peter Cock *Cc:* Galaxy Dev *Subject:* Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.com wrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id
Ok, great, glad that worked for you. And, thanks for the heads up on the actual table name :) -Dannon On Tue, Apr 22, 2014 at 9:14 AM, Lukasse, Pieter pieter.luka...@wur.nlwrote: Hi Dannon, Thanks, this helped. Just for the record: I did find a small typo in my mail and in your script : should be migration_tmp instead of migrate_tmp;) Best regards, Pieter. *From:* Dannon Baker [mailto:dannon.ba...@gmail.com] *Sent:* dinsdag 22 april 2014 14:59 *To:* Lukasse, Pieter *Cc:* Peter Cock; Galaxy Dev *Subject:* Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id Hey Pieter, sure. The sqlite database is in sqlite3 format, so you'll need to use 'sqlite3 database/universe.sqlite' to access it. The following should work: sqlite3 database/universe.sqlite '.dump migrate_tmp' temporary_backup.sql sqlite3 database/universe.sqlite 'drop table migrate_tmp;' And, once that's done, verify that everything works as expected and that whatever table is in temporary_backup.sql actually did get migrated. -Dannon On Tue, Apr 22, 2014 at 8:41 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Dannon, I’m facing the same problem now. Could you help me with the steps to delete the migrate_tmp table manually? I’m trying to use sqlite from command line but get the following error: Unable to open database universe.sqlite: file is encrypted or is not a database Thanks and regards, Pieter. *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Dannon Baker *Sent:* dinsdag 18 februari 2014 14:40 *To:* Peter Cock *Cc:* Galaxy Dev *Subject:* Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.com wrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Hackathon at GCC2014
Galaxy has a fantastic developer community, from the very active mailing lists and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people involved. To that end, we’re thrilled to officially announce the very first Galaxy Hackathon (http://bit.ly/gcc2014hack). The hackathon will be a three day event taking place at Johns Hopkins immediately preceding GCC2014 from June 28th-30th. Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or Cloudman!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at http://bit.ly/gcc2014hackreg. To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using at https://trello.com/b/3YgU637b/gcc2014-hackathon. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that. Finally, we are very happy to have Curoverse (https://curoverse.com) on board as the exclusive Peta level sponsor of the hackathon. If you know of any other group that might be interested in sponsoring at the Giga level please let us know. We hope to see you in June, and can't wait to see what we can accomplish! -Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] how to delete datasets or save space on local galaxy
Hey, sure. The option you're looking for is allow_user_dataset_purge, around line 650 or so. Good luck! -Dannon On Fri, Apr 11, 2014 at 5:53 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Dannon, Could you tell me how to edit the configure file? What I see from here https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets is how to use the command line, correct? Thanks a lot! Best, Xiaofei -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Friday, April 11, 2014 4:42 PM *To:* Wang, Xiaofei *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] how to delete datasets or save space on local galaxy Hi Xiaofei, The (x) simply flags a dataset for deletion, it does not remove it from disk. This happens when the instance maintainers run cleanup scripts. If your instance is so configured, you can use the Purge Deleted Datasets option to immediately remove datasets from disk. -Dannon On Fri, Apr 11, 2014 at 5:33 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, May I ask a question which might be really simple? How to delete a dataset from a history in local Galaxy? When I clicked on delete (x), the size on disk is still the same as before deleting it. Thank you so much! Best, Xiaofei ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ inline: Screen Shot 2014-04-11 at 4.30.18 PM.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] krona to metaphlan patch
Hey Brad, thanks for this! I've added these to the metaphlan toolshed repository as-is, and will be adding tests shortly. On Tue, Apr 8, 2014 at 1:24 AM, Langhorst, Brad langho...@neb.com wrote: I'm running with these local additions to Dannon's metaphlan repo. I think it would be better to add these to the current metaphlan repo than to release them standalone. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
Hey Mo, Sorry for the super delayed response here. I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume. It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section: tool file=data_source/ebi_sra.xml / -Dannon On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes. Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? With everything headed to the toolshed, hopefully this is a thing of the past very soon. The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial In short, you'll need to: 1) ssh to your cloud galaxy instance 2) navigate to /mnt/galaxy/galaxy-app 3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3): tool file=data_source/ebi_sra.xml / 4) Close down ssh, 5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service. One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea. I'll try to document this better. Thanks again, Dannon! Anytime, thanks for your patience and for using Galaxy/Cloudman! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] restarting multiple web workers
On Tue, Apr 1, 2014 at 2:48 PM, Langhorst, Brad langho...@neb.com wrote: However, when i add a new tool - it does not alway show up (only for one of the workers maybe?) I don't have good answers for the rest of your questions (I'm sure someone else can chime in), but I do have some information about this. You're correct in that, currently, the only process that will reflect the new or reloaded tool is the one the admin user was actually interacting with. While it doesn't solve your problem right now, I've been working on new mechanisms for reloading tools and generally interacting with multiple processes that will be available soon. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] I can't impersonate an user
It isn't in galaxy-dist (yet), but it is in the stable branch of
galaxy-central, which is safe to pull into a galaxy-dist based repository.
-Dannon
On Tue, Mar 25, 2014 at 10:13 AM, Eric Kuyt erick...@gmail.com wrote:
Hi Dannon,
could this still be existent in galaxy-dist?
Impersonate.makohttps://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3/templates/admin/impersonate.mako?at=default
doesn't seem to have ${h.url_for(controller=/api/users,
action=index)} in its source and tries to find /api/user on the server
root.
Thanks,
Eric
On 17 March 2014 16:31, Dannon Baker dannon.ba...@gmail.com wrote:
694411e94d9a
___
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Re: [galaxy-dev] I can't impersonate an user
Hi Ricardo, My guess is that you're running into an issue that was fixed in 694411e94d9a. Can you verify the URL that's being pinged by the impersonate dropdown is (in)valid? If so, pulling from stable should fix your issues. -Dannon On Mon, Mar 17, 2014 at 11:24 AM, Perez, Ricardo ricky_...@neo.tamu.eduwrote: Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Empty history pane
Good to hear you've worked around it! For future reference, in Firefox you can open the javascript console by clicking the Firefox (menu at the top)-Web Developer-Web Console. That, or Control/Command+Shift+K. On Fri, Mar 14, 2014 at 1:49 PM, Liisa Koski liisa.ko...@basf.com wrote: Our use was using the lastest Firefox release. I asked him to try FireFox Portable and that seemed to do the trick. It was a problem with his Firefox install. Thanks for you help, Liisa From:Dannon Baker dannon.ba...@gmail.com To:Liisa Koski liisa.ko...@basf.com Cc:Galaxy Dev galaxy-dev@lists.bx.psu.edu Date:13/03/2014 06:39 PM Subject:Re: [galaxy-dev] Empty history pane -- If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski *liisa.ko...@basf.com*liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: *http://lists.bx.psu.edu/* http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: *http://galaxyproject.org/search/mailinglists/*http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Empty history pane
If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Running out of memory on data download
My first guess is that it's likely this is due to 'debug = True' being set in your universe_wsgi.ini. If you set this to false and restart, the entire request will no longer be loaded into memory. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ImportError: No module named json
The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ImportError: No module named json
Got it. We dropped the simplejson egg during the last release (and any you find are holdovers from previous versions of galaxy) in favor of the stdlib module. The relevant module from your find would have been simplejson-2.1.1, and the rest are unrelated. If possible, I'd *really* recommend updating the python version on those nodes as future galaxy developments and tools may count on python 2.6+ (and not just for json, but syntax changes) being available. Other than that, for those affected tools, you may want to manually revert the changes in revision 11967:0c5e20558f6b and add simplejson back into your galaxy. That said, I'm working on adding the anyjson dependency that will allow json to fail through to any installed json library (whether stdlib, simplejson, etc), and that'll be available in galaxy-central reasonably soon. On Thu, Feb 20, 2014 at 2:51 PM, Fenglou Mao feng...@gmail.com wrote: It is a little complicated here, The Galaxy server itself is running CentOS 6 with python 2.6, but the cluster nodes are running CentOS 5 with python 2.4. Mose jobs are running in the cluster nodes. My questions is: if there is a json module in galaxy-dist/eggs, why Galaxy is not picking it up? If we can do this, then we don't need to upgrade the cluster nodes, which is very difficult here. Fenglou On 20 February 2014 13:47, Dannon Baker dannon.ba...@gmail.com wrote: The json module is included in python's standard library since python 2.6, which is the minimum version of python Galaxy currently supports. Are you using a python version older than that? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id
On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote: This fixed the history_dataset_association.extended_metadata_id error - so is the most likely explanation a failed schema update? Might a stale migration_tmp table have been to blame? Yes, I've seen this before when I've killed (or otherwise crashed) a migration in process; migrate_tmp doesn't get automatically cleaned up -- and, to allow for recovery, probably shouldn't.Any idea what may have caused it in your case?For a development database I've most commonly just deleted the migrate_tmp table manually and rerun the migration. It's worth noting that *only* sqlite can have this problem, due to the way migrations work. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] mpileup - ImportError: cannot import name stylesheet_link_tag
Galaxy was recently updated to use a newer version of webhelpers, version 1.3, in which the signatures of those methods have changed. It looks like you're running a newer version of webhelpers (thus stylesheet_link_tag not being found), but an older version of galaxy. I'm not sure how this would be the case, but is it possible for you to update your galaxy and run with a clean environment (using galaxy's provided webhelper egg), to see if this resolves your issue? -Dannon On Fri, Feb 7, 2014 at 12:11 PM, Adhemar azn...@gmail.com wrote: Hi! I was running mpileup and it's showing the error bellow. The strange thing is that 'galaxy/web/framework/helpers/__init__.py' is trying to import 'stylesheet_link_tag' and it's not available in the webhelpers I've installed for both python versions 2.6.6 or 2.7.3 Could you help me with this? Thanx, Adhemar Traceback (most recent call last): File ./scripts/set_metadata.py, line 29, in module import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/model/__init__.py, line 23, in module import galaxy.datatypes.registry File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/registry.py, line 5, in module import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, graph File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/data.py, line 2, in module import metadata File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/metadata.py, line 24, in module from galaxy.web import form_builder File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/__init__.py, line 4, in module from framework import expose File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py, line 28, in module import helpers File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/helpers/__init__.py, line 4, in module from webhelpers import date, stylesheet_link_tag, javascript_include_tag, url_for ImportError: cannot import name stylesheet_link_tag ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] html output with javascript
Hi Laure,
This is intentional behavior; galaxy sanitizes all html output as a
security measure by default. You can turn this off on your instance by
changing sanitize_all_html to False in your universe_wsgi.ini.
There's a Trello card to track implementation of allowing administrators to
individually pick which tools to trust, which you can see (and vote for, or
follow) here: https://trello.com/c/8iMhKlPX
-Dannon
On Wed, Feb 5, 2014 at 9:44 AM, Laure QUINTRIC laure.quint...@ifremer.frwrote:
Hello galaxy users,
one of my tools returns an html output in which I have links to images and
javascripts.
Images and Javascripts of the dataset_XXX.dat file are located in a
dataset_XXX_files directory. Images are well displayed in galaxy output but
javascripts aren't executed. Even an alert('foo') cannot be retrieved.
Has somebody already experiment this ? In other related posts, it's said
to look at rgenetics fastqc wrapper but no javascript fonctions are called
in the fastqc_report.html.
Thanks,
Laure
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Re: [galaxy-dev] Can't view file_name in histories via API unless admin?
Hey Neil, While poking through a few options for you, I remembered we added 'expose_dataset_path' to universe_wsgi.ini. If you're comfortable with users knowing full pathnames, you can enable this 'expose_dataset_path = True' and everyone will be able to see their full paths. -Dannon On Sat, Jan 18, 2014 at 9:37 PM, neil.burd...@csiro.au wrote: Thanks Dannon, Apologies for the length of the email, I'll try and be as succint as possible. I am using Galaxy as a tool for medical image processing. We have a number of organisations (researchers and clinicians ) who would like to use the medical imaging tools we have developed, so are using Galaxy to make them available to the whole community. The researchers and clinicians would just prefer to select a file press execute and then everything would be done i.e. uploaded, processed, results returned. I've managed to achieve this (using a test account which is an admin user). In summary, using John Chilton's multi-file branch of Galaxy, the user can select multiple files and then presses execute. The code(and workflows) then upload all the files selected, splits them into smaller datasets (as the tool only needs 2 input files - for example the user may upload 0179_AV45.hdr, 0179_AV45.img, 0279_AV45.hdr, 0179_AV45.img, 0199_AV45.hdr and 0199_AV45.img, given these 6 input files; 3 datasets will be created based on the filenames i.e. 0199_AV45.hdr and 0199_AV45.img will be in one dataset etc). Another tool is responsible for batching and executing the medical imaging tool with each of these 3 datasets, and finally all the results are returned and then emailed back to the user ( so no user interaction is required other than selecting files and pressing execute) This all worked fine as an admin user, but as a non admin user we are unable to get the file_name from the /api/histories/contents/ etc... being upload for the dataset_id.dat. We need to get the history id of that datase_id.dat filename so we can execute the workflow. As admin, I have a script that is able to get get all the files uploaded (under/histories/contents/etc ...) and then examine each history id to get the file_name and match it with the name that we just uploaded. From this we could then get the history_id. But seen as we can't get hold of the file_name unless your an admin user. Do you know how we can get hold of the history_id of the filename i.e. we can't just assume it's the last entry in /history/contents. So given only a database_'id'.dat filename how can I get the history id dynamically with no user interaction and not being an admin user? Thanks for any help Neil p.s. do you know where in the code it stops file_name from being displayed (using the scripts/api/display.py script) -- *From:* Dannon Baker [dannon.ba...@gmail.com] *Sent:* Saturday, January 18, 2014 12:34 AM *To:* Burdett, Neil (CCI, Herston - RBWH) *Cc:* charles.girar...@embl.de; Galaxy Dev *Subject:* Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Niel, Galaxy does not expose filepaths to non-admin users intentionally. For executing a workflow with that particular script, the 'file_id' in question in that example should be an hda, which is what api/history/contents will display for your users as the 'id' for each history item. -Dannon On Fri, Jan 17, 2014 at 6:12 AM, neil.burd...@csiro.au wrote: Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The api_key in your question refers to the api_key of an admin user, however, the history_id (ebfb8f50c6abde6d) refers to a history not owned by the admin user using the unique api_key i.e. another user, hence the error message I hope that answers your question? Neil From: Charles Girardot [charles.girar...@embl.de] Sent: Friday, January 17, 2014 6:31 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Neil, sorry, this is not an answer to your post, I hope you won t mind me stepping in your thread this way. Your message kept my attention because of your note: I am surprised by the error message you report when trying to use an admin API key. How does galaxy know the user who is making the call? Sorry if I am missing the obvious bw Charles On 17 Jan 2014, at 07:35, neil.burd...@csiro.au wrote: Hi, it seems that the entry file_name: does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin
Re: [galaxy-dev] Can't view file_name in histories via API unless admin?
Hi Niel, Galaxy does not expose filepaths to non-admin users intentionally. For executing a workflow with that particular script, the 'file_id' in question in that example should be an hda, which is what api/history/contents will display for your users as the 'id' for each history item. -Dannon On Fri, Jan 17, 2014 at 6:12 AM, neil.burd...@csiro.au wrote: Hi Charles, not a problem. In my previous post I specified the command line: /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 The api_key in your question refers to the api_key of an admin user, however, the history_id (ebfb8f50c6abde6d) refers to a history not owned by the admin user using the unique api_key i.e. another user, hence the error message I hope that answers your question? Neil From: Charles Girardot [charles.girar...@embl.de] Sent: Friday, January 17, 2014 6:31 PM To: Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can't view file_name in histories via API unless admin? Hi Neil, sorry, this is not an answer to your post, I hope you won t mind me stepping in your thread this way. Your message kept my attention because of your note: I am surprised by the error message you report when trying to use an admin API key. How does galaxy know the user who is making the call? Sorry if I am missing the obvious bw Charles On 17 Jan 2014, at 07:35, neil.burd...@csiro.au wrote: Hi, it seems that the entry file_name: does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py api_key http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin user in the universe_wsgi.ini i.e. admin_users = t...@test.com,te...@test.com is this known? Is there anyway to get around this as we don't want all users to be admin, however, they need access to this field. Note that you can't use an admin's api_key as you'll get the error Error in history API at listing dataset: History is not owned by the current user Thanks Neil ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] allow_user_impersonation (was: creating a hierarchy of students teachers and courses)
Imagine that, actually two cards for it! On Thu, Jan 16, 2014 at 8:33 AM, John Chilton chil...@msi.umn.edu wrote: Card exists and it has 10 votes, that is the most I have seen in a while. https://trello.com/c/zwqNwflD I have added myself as a member to the card, I will see if I can find some time to work on this. -John On Thu, Jan 16, 2014 at 7:27 AM, Dannon Baker dannon.ba...@gmail.com wrote: On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: allow_user_impersonation does not work when using external authentication. Are there any fixes for this in progress? If not shall I create a Trello card? If there's no Trello card for it, I doubt it's currently being worked on. And, of course, feel free! -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Linking Data Files
On Wed, Jan 15, 2014 at 3:04 PM, Cantarel, Brandi L. brandi.canta...@baylorhealth.edu wrote: I can see where I can upload libraries from the galaxy server, but I can’t figure out how to load the “available” data (fastqs) — to clarify instead of asking users to upload 5GB fastq files, which are already on the galaxy server, I would like for users to be able to “see” that data when setting up their pipeline without having to upload the data (ie use Get Data). Is this possible? When I search, I can only see how to do this for “Data Libraries”. Data Libraries are probably the right way to handle this. If you have a large set of fastq data, would it be sufficient to load it all into a data library accessible to your users? Then the user would just have to browse the data library, click import to current history, and they're off and running. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
