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] galaxy server file upload problem
Thanks for your reply Danon I have tried to setup local galaxy-server in production mode The error that I mentioned occurred when I tried to upload file from my pc to local galaxy server( galaxy server is also installed in same pc ) and my galaxy server is at the root of the domain ( http://127.0.0.1:8080) the attached file is screenshot of error and the other attached file is my nginx configuration file Thanks for your effort in helping me Regards Jonghui - Original Message - From:Dannon Baker [dannon.ba...@gmail.com] To:홍종희 [h...@syntekabio.com] Cc:Galaxy Dev [galaxy-dev@lists.bx.psu.edu] Sent:Wed , November 19, 2014 23:19 PM Subject: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/
[galaxy-dev] galaxy server file upload problem
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/
Re: [galaxy-dev] Galaxy Data Sources and Dataset Collections
These are all good ideas but I don't think any of the constituent parts are currently possible (symbolic linking outside of libraries, tools that create collections, data sources that create collections, starting workflows with data source tools - there is some bug that prevents GenomeSpace from working for instance). If you are developing something from the ground up - you may want to just drive this all externally with the API - you create create library datasets that are linked, move them into a history and create a collection, send that collection into a workflow - this is all doable but would mean building an external UI for running workflows :(. Sorry I don't have better news. Would love pull requests to address some of these issues - but it is a lot of work. -John On Mon, Nov 10, 2014 at 2:29 PM, Aaron Petkau aaron.pet...@gmail.com wrote: Hello, I've been spending a bit of time looking over Data Sources for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Galaxy, along with some user credentials. In this sense it would be similar to the GenomeSpace importer tool. However, instead of just exporting a set of files to a user's history, I'd like to be able to also automatically group these files into a dataset collection. I would also like to be able to link to these files instead of creating copies (which I think I can only do through a Data Library am I correct?). Ideally, I'd like to be able to use this tool as the first step in a workflow, which would allow me to import and structure the data needed for the rest of the workflow. Does anyone have any experience writing a similar tool? Is this possible in the current Galaxy version? Thanks, Aaron ___ 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/
[galaxy-dev] Galaxy Mailing Lists are moving
Hello Galaxy Community, *Galaxy Mailing Lists are moving!* During the week of November 17-21, 2014, Galaxy mailing lists (including this one) will be migrated from lists.bx.psu.edu to lists.galaxyproject.org . This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu to galaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. As always, you can manage your subscription for any Galaxy mailing list by following the link instructions at the bottom of this announcement. If you should notice any problems after the migration, please do not hesitate to let us know, via email to both list-ow...@lists.galaxyproject.org (after the move) and to myself. Thanks, --nate, and the Galaxy Team ___ 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 Data Sources and Dataset Collections
Hello, I've been spending a bit of time looking over Data Sources https://wiki.galaxyproject.org/Admin/Internals/DataSources for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Galaxy, along with some user credentials. In this sense it would be similar to the GenomeSpace https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/tools/genomespace/?at=default importer tool. However, instead of just exporting a set of files to a user's history, I'd like to be able to also automatically group these files into a dataset collection. I would also like to be able to link to these files instead of creating copies (which I think I can only do through a Data Library am I correct?). Ideally, I'd like to be able to use this tool as the first step in a workflow, which would allow me to import and structure the data needed for the rest of the workflow. Does anyone have any experience writing a similar tool? Is this possible in the current Galaxy version? Thanks, Aaron ___ 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
Hi Dannon, Clearing the browser cache worked! Thanks so much. Jeremy Liu On Thu, Nov 6, 2014 at 2:04 AM, ofer fridman ofer.frid...@mail.huji.ac.il wrote: I Had the same problem, after moving to stable everything is working. I know it's not a solution but for the meantime this is what I have. Best, Ofer On Wed Nov 05 2014 at 11:04:01 PM Dannon Baker dannon.ba...@gmail.com wrote: 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/ ___ 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 Not Displacing History
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/
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/
[galaxy-dev] Galaxy with Rocks Cluster / Submitting Job As Real User
Hi, I've been trying to get Galaxy to submit jobs to my cluster as the real user rather than the galaxy user. In my galaxy.ini, I have: outputs_to_working_directory = True set_metadata_externally = True drmaa_external_runjob_script = /galaxy/scripts/drmaa_external_runner.py drmaa_external_killjob_script = /galaxy/scripts/drmaa_external_killer.py drmaa_external_chown_script = /galaxy/scripts/external_chown_script.py In my sudoers file I have: galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/drmaa_external_runner.py galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/drmaa_external_killer.py galaxy ALL= (root) NOPASSWD: SETENV: /galaxy/scripts/external_chown_script.py In my log file, I'm seeing: galaxy.jobs.runners.drmaa DEBUG 2014-10-29 14:45:54,777 (15) submitting file /galaxy/database/job_working_directory/000/15/galaxy_15.sh galaxy.jobs.runners.drmaa DEBUG 2014-10-29 14:45:54,783 (15) submitting with credentials: tjg [uid: 28369] galaxy.jobs.runners ERROR 2014-10-29 14:45:54,784 (15) Unhandled exception calling queue_job Traceback (most recent call last): File /galaxy/lib/galaxy/jobs/runners/__init__.py, line 96, in run_next method(arg) File /galaxy/lib/galaxy/jobs/runners/drmaa.py, line 189, in queue_job filename = self.store_jobtemplate(job_wrapper, jt) File /galaxy/lib/galaxy/jobs/runners/drmaa.py, line 348, in store_jobtemplate f = open(filename,'w') IOError: [Errno 2] No such file or directory: '/galaxy/database/pbs/15.jt_json' My /var/log/messages file is not reporting any attempt to run sudo, so I think the process is failing before it gets to that point in the Galaxy code. If I comment out the drmaa_external_* lines, the jobs are submitted successfully and run as the galaxy user. What am I missing here? :) -- Tim Gustafson t...@ucsc.edu 831-459-5354 Baskin Engineering, Room 313A ___ 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 instance file upload problem
As Hans said, this might reguire a change in the proxy server configuration as discussed here: http://gmod.827538.n3.nabble.com/Data-uploaded-with-new-upload-tool-doesn-t-get-added-to-history-td4046375.html On Fri, Oct 17, 2014 at 2:43 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Bongsoo we had once a similar situation with one of our development Galaxy installations. This was due to a change in the proxy settings of the server. Regards, Hans-Rudolf On 10/17/2014 01:06 AM, Bongsoo Park wrote: Aysam, Thanks for your reply. It works well on usegalaxy.org http://usegalaxy.org, but it doesn't work in the Galaxy instance I've developed. I downloaded the latest Galaxy version, and installed on the Redhat 6.5 system. I created a galaxy user, and just ran it as usual. I have to update any part of the configuration? I have to allow any specific port to use file upload function? Thanks! Best, Bongsoo On Thu, Oct 16, 2014 at 6:25 PM, Aysam Guerler aysam.guer...@gmail.com mailto:aysam.guer...@gmail.com wrote: Hey Bongsoo, Does this happen on usegalaxy.org http://usegalaxy.org? Also does this happen with other files too? Thanks, Sam On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park bx...@psu.edu mailto:bx...@psu.edu wrote: Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ 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] Galaxy instance file upload problem
Hi Bongsoo we had once a similar situation with one of our development Galaxy installations. This was due to a change in the proxy settings of the server. Regards, Hans-Rudolf On 10/17/2014 01:06 AM, Bongsoo Park wrote: Aysam, Thanks for your reply. It works well on usegalaxy.org http://usegalaxy.org, but it doesn't work in the Galaxy instance I've developed. I downloaded the latest Galaxy version, and installed on the Redhat 6.5 system. I created a galaxy user, and just ran it as usual. I have to update any part of the configuration? I have to allow any specific port to use file upload function? Thanks! Best, Bongsoo On Thu, Oct 16, 2014 at 6:25 PM, Aysam Guerler aysam.guer...@gmail.com mailto:aysam.guer...@gmail.com wrote: Hey Bongsoo, Does this happen on usegalaxy.org http://usegalaxy.org? Also does this happen with other files too? Thanks, Sam On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park bx...@psu.edu mailto:bx...@psu.edu wrote: Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ 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] galaxy-dev Digest, Vol 100, Issue 10
So I have finally determined the cause and found a resolution. The issue was the fact that the version of Java on the Ubuntu linux VM from AWS is 1.6.x. GATK2 requires version 1.7.0 or higher. This is fine, but you will need to manually upgrade the java version. To do so you will need to complete the following: SSH to the VM sudo su - root CD to /mnt/galaxy/ Complete the following steps: 1. sudo apt-get purge openjdk* (This removes java 1.6 completely) 2. Modify this file: vi /etc/apt/sources.list.d/cloudbiolinux.list (Remove the leading section of line 11) 3. sudo add-apt-repository ppa:webupd8team/java 4. sudo apt-get update 5. sudo apt-get install oracle-java7-installer 6. java -version Now if you plan to add nodes via the Cloudman Console you will need to perform these tasks for each node you install. I worked with AWS Support to setup an Auto Scaling Group to accommodate this process. This required getting my Master instance upgraded and creating an AMI from it. From that point you can build the group based on the following: http://docs.aws.amazon.com/AutoScaling/latest/DeveloperGuide/creating-your- auto-scaling-groups.html This was, in theory, a great idea. However, it did not work for me. Each of the node that were generated by this tool had Java version 1.6.x and this caused GATK2 to fail. My recommendation is that if you have time you should paly around with this more, but I did not have that luxury for this project. Iry On 10/11/14 12:00 PM, galaxy-dev-requ...@lists.bx.psu.edu galaxy-dev-requ...@lists.bx.psu.edu wrote: Send galaxy-dev mailing list submissions to galaxy-dev@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-requ...@lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-ow...@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than Re: Contents of galaxy-dev digest... HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Re: Tool development: Is it possible to pass a user's id in dynamic_options() parameter? (Dooley, Damion) 2. Re: Tool development: Is it possible to pass a user'sid in dynamic_options() parameter? (Daniel Blankenberg) 3. Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 4. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 5. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 6. Re: Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 7. Re: Anyone else having issues with cloudman cloudlaunch? (Dannon Baker) 8. Re: Anyone else having issues with cloudman cloudlaunch? (Chris Dagdigian) 9. GATK2 java version related issues (Iry Witham) 10. Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client? (Chris Dagdigian) 11. Re: GATK2 java version related issues (Daniel Blankenberg) 12. Re: Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc client? (Dannon Baker) 13. Re: GATK2 java version related issues (Iry Witham) -- Message: 1 Date: Fri, 10 Oct 2014 09:02:50 -0700 From: Dooley, Damion damion.doo...@bccdc.ca To: Daniel Blankenberg d...@bx.psu.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a user's id in dynamic_options() parameter? Message-ID: 7891813f3c8f424b97d8bf2e5600e51903302322c...@vexccr02.phsabc.ehcnet.ca Content-Type: text/plain; charset=Windows-1252 Hi Dan, I'd like to get the user's galaxy user name directly - but the code file=... that drives my dynamic_options select list has no access to any information in a galaxy's user session, right? (Ultimately I'm trying to get the dynamic_options code to make galaxy api calls using the user's api key.) I saw the GenomeSpace tool earlier - but got the impression that a user was entering their genome login in the tool form. I was hoping just to get a user's galaxy id without any re-entry of it. p.s. Its been really great getting advice from all of you; I hope to contribute likewise. d. Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control
Re: [galaxy-dev] galaxy-dev Digest, Vol 100, Issue 15
So Ihave finally determined the cause and found a resolution for the
snpEff/java problem. The issue was the fact that the vrsion of Java on
the Ubuntu linux VM from AWS is 1.6.x snpEff 4.0e requires version 1.7.0
or higher. This is fine, but you willneed to manually upgrade the java
version. To do so you will need to complete the following:
SSH to the VM
sdo su - root
CD to /mnt/galaxy/
Complete the following steps:
1. sudo apt-get purge openjdk* (This removes java 1.6 completely)
2. Modify this file: vi /etc/apt/sources.list.d/cloudbiolinu.list
(Remove the leading section of line 11)
3. sudo add-apt-repository ppa:webupd8team/java
4. sudo apt-get update
5. sudo apt-get installoracle-java7-installer
6. java -version
Now if you plan to add nodes via the Cloudman Console you will need to
perform these tasks for each node you install. I worked with AWS Support
to setup an Auto Scaling Group to accommodate this process. This
required getting my Master instance upgraded and creating an AMI from it.
From that point you can build the group based on the following:
http://docs.aws.amazon.com/AutoScaling/latest/DeveloperGuide/creating-your-
auto-scaling-groups.html
This was, in theory, a great idea. However, it did not work for me. Each
of the node that were generated by this tool had Java version 1.6.x and
this caused snpEff t fail. My recommendation is that if you have time
you should paly around with this more, but I did not have that luxury for
this project.
Iry
On 10/16/14 12:00 PM, galaxy-dev-requ...@lists.bx.psu.edu
galaxy-dev-requ...@lists.bx.psu.edu wrote:
Send galaxy-dev mailing list submissions to
galaxy-dev@lists.bx.psu.edu
To subscribe or unsubscribe via the Worl Wide Web, visit
http://lists.bx.psu.edu/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
galaxy-ev-requ...@lists.bx.psu.edu
You can reach the person managing the list at
galaxy-dev-ow...@lists.bx.psu.edu
When replying, please edit your Subjct line so it is more specific
than Re: Contents of galaxy-dev digest...
HEY! This is important! If you reply to a thread in a igest, please
1. Change the subject of your response from Galaxy-dev Digest Vol ...
to the original subject for the thread.
2. Strip out everything else in the dgest that is not part of the thread
you are responding to.
Why?
1. This will keep the subject meaningful. People will have some ideafrom the
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match
search ueries, but that aren't actually informative.
Today's Topics:
1. Re: Set output dbkey from parameter value (Daniel Blankenberg) 2. Re:
Set output dbkey from parameter value (Nikos Sidiropoulos)
3. Re: snpeff tool for Galay extra_files_path (John Chilton)
4. Re: snpeff tool for Galaxy extra_files_path (Bj?rn Gr?nng)
5. Re: snpeff tool for Galaxy extra_files_path (John Chilton)
6. Re: snpeff tool for Galaxy extra_files_path (Jim Johnson)
7. snpEff and java issue(Iry Witham)
8. Re: HOWTO share tool parameter settings? (Lukasse, Pieter)
9.Help with Galaxy server migration (Sarah Diehl)
10. Re: Help with Galaxy server migrtion (John Chilton)
11. Login issue with a nginx proxy (Alexandre Loywick)
12. Re: Help with Galaxy server migration (Sarah Diehl)
-
Message: 1
Date: Wed, 15 Oct 2014 12:14:28 -0400
From: Daniel Blankenberg d...@bx.psu.edu
To: Nikos Sidiropoulos nikos.sid...@gmail.com
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Set output dbkey from parameter value
Message-ID: e77c8a92-617a-455e-b5eb-209f4505b...@bx.psu.edu
Content-Type: text/plain; charset=windows-1252
Does removing the ?param_attribute=?value' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi Daniel,
Thanks for the response.
I've edited the output to:
data format=bedgraph name=bedgraph_slograt
label=${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)
from_work_dir=output_dir/slograt.bedgraph
filter bedgraph['check'] == 'yes' and slograt['check']
== 'yes' /filter
actions
conditional name=bedgraph.check
when value=yes
action type=metadata name=dbkey
option type=from_param
name=bedgraph.genome param_attribute=value /
/action
/when
/conditional
/actions
/data
Now I'm getting a tool execution error.
Error executing tool: 'unicode' object has no attribute 'value'
I've tried to change the param_attribute to ext, dbkey (ones that
I know that exist) and got a similar error.
Bests,
Nikos
On 15 October 2014 16:58, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Nikos,
In the very least, you?ll want to make sure
[galaxy-dev] Galaxy Training Network
Hello all, We are pleased to announce the *Galaxy Training Network (GTN) https://wiki.galaxyproject.org/Teach/GTN*, a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers https://wiki.galaxyproject.org/Teach/Trainers, and to share and discover the wealth of training resources available for Galaxy. This includes training materials https://wiki.galaxyproject.org/Teach/Resources, a trainer directory https://wiki.galaxyproject.org/Teach/Trainers,best practices https://wiki.galaxyproject.org/Teach/BestPractices, and guidance on computing platforms https://wiki.galaxyproject.org/Teach/ComputingPlatforms for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community. If you teach with Galaxy, then please consider adding your organization https://wiki.galaxyproject.org/Teach/Trainers#Add_a_Trainer, materials https://wiki.galaxyproject.org/Teach/Resources#Add_a_Training_Resource, and best practices https://wiki.galaxyproject.org/Teach/BestPractices. The Trainer Directory https://wiki.galaxyproject.org/Teach/Trainers already includes 16 organizations and there may be one (or 6!) near you http://bit.ly/gxytrnmap. Thanks, The Galaxy Training Network (GTN) https://wiki.galaxyproject.org/Teach/Trainers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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 instance file upload problem
Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ 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 instance file upload problem
Hey Bongsoo, Does this happen on usegalaxy.org? Also does this happen with other files too? Thanks, Sam On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park bx...@psu.edu wrote: Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ 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 instance file upload problem
Aysam, Thanks for your reply. It works well on usegalaxy.org, but it doesn't work in the Galaxy instance I've developed. I downloaded the latest Galaxy version, and installed on the Redhat 6.5 system. I created a galaxy user, and just ran it as usual. I have to update any part of the configuration? I have to allow any specific port to use file upload function? Thanks! Best, Bongsoo On Thu, Oct 16, 2014 at 6:25 PM, Aysam Guerler aysam.guer...@gmail.com wrote: Hey Bongsoo, Does this happen on usegalaxy.org? Also does this happen with other files too? Thanks, Sam On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park bx...@psu.edu wrote: Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ 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/
[galaxy-dev] Galaxy database corrupted
Recently I tried to upload some annotation/reference files into Galaxy. After couple failed tries using the upload method, I was able to do it via the using the full file path. However, after these tries/retries, I believe Galaxy database got confused and was corrupted. Existing workflows with existing reference were used when datasets that previously were processed without any problems, now have funky result set names and parameters to tool wrappers reference funky paths. Here’s an example of the error I’m encountering. The highlighted part references the dbSNP file: python /home/svcbioinfo/galaxy/galaxy-reproduce/tools/gatkV2/gatk_wrapper.py --max_jvm_heap 16g --max_jvm_heap_fraction 1 --stdout /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24218.dat -d -I /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24216.dat bam gatk_input_first -d /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/_metadata_files/001/metadata_1491.dat bam_index gatk_input_first -p 'java -jar /home/svcbioinfo/galaxy/galaxy-reproduce/tool-data/shared/jars/gatk/GenomeAnalysisTKv2.jar -T RealignerTargetCreator --num_threads 4 -o /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24217.dat -et NO_ET -K /home/svcbioinfo/galaxy/galaxy-reproduce/tool-data/shared/jars/genomichealth.com.key -R /mnt/ngs/analysis/refData/processed/bwa/hg19_decoy_rcrs8001sp.fasta ' -d -known:dbsnp,%(file_type)s /mnt/ngs/analysis/tchu/Workflow_RWC/SEQUENCER99/140201_SNTEST_0021_TESTFC21/analysis_31/primary/fastq/99_21_3_ACAGTG_R2.fastq fastq input_dbsnp_0 -d -known:indels,%(file_type)s /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/016/dataset_16596.dat vcf input_indels_0 -p '--pedigreeValidationType STRICT' -d --intervals /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/022/dataset_22821.dat bed input_intervals_0 -p '--interval_padding 400' -p '--interval_set_rule UNION' -p '--downsampling_type NONE' -p ' --validation_strictness SILENT --interval_merging ALL ' -p ' --unsafe LENIENT_VCF_PROCESSING The highlighted part should be the dbSNP file which typically has a Galaxy based name and type of “vcf” such as below: python /home/svcbioinfo/galaxy/galaxy-reproduce/tools/gatkV2/gatk_wrapper.py --max_jvm_heap 16g --max_jvm_heap_fraction 1 --stdout /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24314.dat -d -I /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24312.dat bam gatk_input_first -d /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/_metadata_files/001/metadata_1492.dat bam_index gatk_input_first -p 'java -jar /home/svcbioinfo/galaxy/galaxy-reproduce/tool-data/shared/jars/gatk/GenomeAnalysisTKv2.jar -T RealignerTargetCreator --num_threads 4 -o /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/024/dataset_24313.dat -et NO_ET -K /home/svcbioinfo/galaxy/galaxy-reproduce/tool-data/shared/jars/genomichealth.com.key -R /mnt/ngs/analysis/refData/processed/bwa/hg19_decoy_rcrs.fasta ' -d -known:dbsnp,%(file_type)s /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/016/dataset_16598.dat vcf input_dbsnp_0 -d -known:indels,%(file_type)s /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/016/dataset_16596.dat vcf input_indels_0 -p '--pedigreeValidationType STRICT' -d --intervals /mnt/ngs/analysis/svcbioinfo/DATA_reproduce/files/016/dataset_16617.dat bed input_intervals_0 -p '--interval_padding 400' -p '--interval_set_rule UNION' -p '--downsampling_type NONE' -p ' --validation_strictness SILENT --interval_merging ALL ' -p ' --unsafe LENIENT_VCF_PROCESSING I wonder if there's a way to recover from this or I'll have to reinstall the database. Thanks for your help. Thuy-Linh Chu ___ 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 Bioblend option for importing dataset into a library?
Il giorno gio, 02/10/2014 alle 16.50 -0700, Dooley, Damion ha scritto: I see Galaxy API has a feature to import a history dataset into the library (in copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as well via Bioblend? Latest docs don't seem to include this feature. It would be the opposite of Bioblend's upload_dataset_from_library(history_id, lib_dataset_id) ) Hi Damion, indeed this feature is not in BioBlend yet, but I have it in my TODO list because we also need it. Hopefully I'll soon have some time to implement the method, test it and open a PR. Best, Nicola Objective is to get customized blast indexes into library that way for shared use. Or have them actually exist outside galaxy, and linked in. Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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/
[galaxy-dev] Galaxy Bioblend option for importing dataset into a library?
I see Galaxy API has a feature to import a history dataset into the library (in copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as well via Bioblend? Latest docs don't seem to include this feature. It would be the opposite of Bioblend's upload_dataset_from_library(history_id, lib_dataset_id) ) Objective is to get customized blast indexes into library that way for shared use. Or have them actually exist outside galaxy, and linked in. Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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 and object stores
Hi Inge, There is an implementation for using the AWS S3 object store as the data store for a given Galaxy instance. The implementation is located here https://bitbucket.org/galaxy/galaxy-central/src/3a51eaf209f2502bf32dbb421ecabb7fe46243ea/lib/galaxy/objectstore/s3.py?at=default and it offers several config options in universe_wsgi.ini. The data stored in S3 is locally cached while it's being operated on but always synced with the back end object store. Pulsar seems to have some support for S3 but, as the docs say in the implementation, it's explicitly beta: https://github.com/galaxyproject/pulsar/blob/b32b7caafc6582a3a28e694e2dbb75e7a8f2bffc/galaxy/objectstore/pulsar.py As a side note, there are some planned enhancements to how the object store implementation is handled and there will hopefully be quite a bit of activity on this topic in the near future (eg, https://trello.com/c/YynQKq8m ). Hope this at least clarifies the state of object store support, Enis On Mon, Aug 25, 2014 at 10:24 AM, Raknes Inge Alexander inge.a.rak...@uit.no wrote: I have a few questions about object stores in Galaxy: 1: Can all Galaxy data sets be stored in an object store? 2: If so, does Galaxy still need to maintain a local copy of the data? 3: Is LWR or Pulsar able to get the data directly from the object store, or does it still have to go through Galaxy? We are planning to let users of our Galaxy installation handle large input/output files (~30G) and we expect that the VM containing our Galaxy installation will become a bottleneck if all data needs to travel through that node. - Inge Alexander Raknes ___ 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 and object stores
Thanks Enis, just to elaborate on Pulsar - I suspect it would work with something like configuring Galaxy with S3 object store right now - but it would do so by having Galaxy cache the data locally and then Pulsar would negotiate the transfer with Galaxy (many different ways this could occur depending on who things are mounted). Ideally - it wouldn't happen this way though - I would love it if Galaxy could determine the job is going to be run remotely and not attempt the cache and then configure the remote Pulsar to cache the file directly from the object store abstraction. In addition to eliminating the extra cache and transfer, it could allow Pulsar and Galaxy to have different views of the underlying data sources (e.g. here the data is mounted as X and there the data is mounted as Y - or here the data is directly available and there get it via IRODS, etc...). There are some ... initial grasps... at this sort of thing in Pulsar and Galaxy but it is not fully (or even substantially) implemented currently. -John On Tue, Aug 26, 2014 at 11:18 AM, Enis Afgan afg...@gmail.com wrote: Hi Inge, There is an implementation for using the AWS S3 object store as the data store for a given Galaxy instance. The implementation is located here https://bitbucket.org/galaxy/galaxy-central/src/3a51eaf209f2502bf32dbb421ecabb7fe46243ea/lib/galaxy/objectstore/s3.py?at=default and it offers several config options in universe_wsgi.ini. The data stored in S3 is locally cached while it's being operated on but always synced with the back end object store. Pulsar seems to have some support for S3 but, as the docs say in the implementation, it's explicitly beta: https://github.com/galaxyproject/pulsar/blob/b32b7caafc6582a3a28e694e2dbb75e7a8f2bffc/galaxy/objectstore/pulsar.py As a side note, there are some planned enhancements to how the object store implementation is handled and there will hopefully be quite a bit of activity on this topic in the near future (eg, https://trello.com/c/YynQKq8m). Hope this at least clarifies the state of object store support, Enis On Mon, Aug 25, 2014 at 10:24 AM, Raknes Inge Alexander inge.a.rak...@uit.no wrote: I have a few questions about object stores in Galaxy: 1: Can all Galaxy data sets be stored in an object store? 2: If so, does Galaxy still need to maintain a local copy of the data? 3: Is LWR or Pulsar able to get the data directly from the object store, or does it still have to go through Galaxy? We are planning to let users of our Galaxy installation handle large input/output files (~30G) and we expect that the VM containing our Galaxy installation will become a bottleneck if all data needs to travel through that node. - Inge Alexander Raknes ___ 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/
[galaxy-dev] Galaxy and object stores
?I have a few questions about object stores in Galaxy: 1: Can all Galaxy data sets be stored in an object store? 2: If so, does Galaxy still need to maintain a local copy of the data? 3: Is LWR or Pulsar able to get the data directly from the object store, or does it still have to go through Galaxy? We are planning to let users of our Galaxy installation handle large input/output files (~30G) and we expect that the VM containing our Galaxy installation will become a bottleneck if all data needs to travel through that node. - Inge Alexander Raknes ___ 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 and HTTPS User-authentification
On Aug 20, 2014, at 3:53 AM, Matthias Enders m.end...@german-seed-alliance.de wrote: Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authentification like described here (https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases): Is there any way of using https or an encryption-method for sending user email and password. Hi Matthias, You can still serve Galaxy over HTTPS by placing it behind a proxy, even if you do not intend to perform authentication in the proxy. You'll just need to set X-URL-SCHEME in the proxy, as documented: For nginx: https://wiki.galaxyproject.org/Admin/Config/nginxProxy For Apache: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy --nate With kind regards, Matthias Enders ___ 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/
[galaxy-dev] Galaxy and HTTPS User-authentification
Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authentification like described here (https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases): Is there any way of using https or an encryption-method for sending user email and password. With kind regards, Matthias Enders ___ 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 dont work on my Bio-Linux
Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can help you. Sincerely Yan Qiao ___ 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 dont work on my Bio-Linux
Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can help you. Sincerely Yan Qiao ___ 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
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/
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] Galaxy error
Hi Emily,
We might be able to track this down on our side if you provide the URL and HTTP
method that caused this error and the time it occurred at.
Thanks,
--nate
On Aug 11, 2014, at 9:20 AM, John Chilton jmchil...@gmail.com wrote:
Hello,
Sorry for the delay - please keep all correspondences on galaxy-dev to
maximize the likelihood someone will respond and respond promptly. I do not
know what would cause this error - does anyone else have any ideas?
-John
On Mon, Aug 4, 2014 at 2:07 PM, Beck, Emily A emily-b...@uiowa.edu wrote:
Sorry for my delayed response. The error is on the main public server, and
happens when I try to map with Bowtie for Illumina. Thank you.
~Emily
Emily Beck
PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
From: John Chilton [jmchil...@gmail.com]
Sent: Tuesday, July 22, 2014 4:06 PM
To: Beck, Emily A
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy error
Hello,
Thanks for the bug report. Is this on the main public server (usegalaxy.org)
or a local instance at the University of Iowa?
-John
On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A emily-b...@uiowa.edu wrote:
Hello,
I have repeatedly gotten the following error message when attempting to use
both the mapping and pileup functions in Galaxy. I am using files that I
have previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user
username emilybeck
quota_percent 19
total_disk_usage 52086193970
nice_total_disk_usage 48.5 GB
email emily-b...@uiowa.edu
is_admin false
tags_used
model_class User
id03f0554e2314759e
sourceHDACollection(f313d1d65c4ee57e,451)
xhr
readyState4
responseText {err_msg: Uncaught exception in exposed API method:,
err_code: 0}
responseJSON
err_msg Uncaught exception in exposed API method:
err_code 0
status500
statusTextInternal Server Error
responseHeaders
Servernginx/1.4.7
Date Wed, 16 Jul 2014 15:19:52 GMT
Content-Type application/json
Transfer-Encoding chunked
Connectionkeep-alive
Cache-Control max-age=0,no-cache,no-store
options
data
parse true
emulateHTTP false
emulateJSON false
Emily Beck
PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
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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] Galaxy error
Hello,
Sorry for the delay - please keep all correspondences on galaxy-dev to
maximize the likelihood someone will respond and respond promptly. I do not
know what would cause this error - does anyone else have any ideas?
-John
On Mon, Aug 4, 2014 at 2:07 PM, Beck, Emily A emily-b...@uiowa.edu wrote:
Sorry for my delayed response. The error is on the main public server,
and happens when I try to map with Bowtie for Illumina. Thank you.
~Emily
*Emily Beck *PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
--
*From:* John Chilton [jmchil...@gmail.com]
*Sent:* Tuesday, July 22, 2014 4:06 PM
*To:* Beck, Emily A
*Cc:* galaxy-...@bx.psu.edu
*Subject:* Re: [galaxy-dev] Galaxy error
Hello,
Thanks for the bug report. Is this on the main public server (
usegalaxy.org) or a local instance at the University of Iowa?
-John
On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A emily-b...@uiowa.edu
wrote:
Hello,
I have repeatedly gotten the following error message when attempting to
use both the mapping and pileup functions in Galaxy. I am using files that
I have previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user username emilybeck quota_percent 19 total_disk_usage 52086193970
nice_total_disk_usage 48.5 GB email emily-b...@uiowa.edu is_admin false
tags_usedmodel_class User id 03f0554e2314759esource
HDACollection(f313d1d65c4ee57e,451) 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 0status
500 statusText Internal Server Error responseHeaders Server nginx/1.4.7
Date Wed, 16 Jul 2014 15:19:52 GMT Content-Type application/json
Transfer-Encoding chunked Connection keep-alive Cache-Control
max-age=0,no-cache,no-store
options dataparse true emulateHTTP false emulateJSON false
*Emily Beck *PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
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Re: [galaxy-dev] Galaxy Security Vulnerability
Does this apply to all past galaxy installs? I have an older galaxy site I've been wanting to phase out rather than upgrade. For now I'd like to use a patch but site version (parent: 7148:17d57db9a7c0 ) predates any of the tags. I presume I'd have to just implement the patch by hand? Regards, Damion Message: 7 Date: Thu, 31 Jul 2014 14:55:57 -0400 From: Nate Coraor n...@bx.psu.edu To: Galaxy Development galaxy-dev@lists.bx.psu.edu, galaxy-annou...@lists.bx.psu.edu Subject: [galaxy-dev] Galaxy Security Vulnerability Message-ID: d482333d-384e-49c8-8dd8-c752e4b0a...@bx.psu.edu Content-Type: text/plain; charset=us-ascii A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python pickle functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability. ... - pickle-2013.01.13.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.01.13 up to 2013.08.12, and possibly older versions of Galaxy as well. Available at: https://depot.galaxyproject.org/patch/pickle-2013.01.13.patch ___ 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 install nginx
dear sir: nginx postgress galaxy which one first install ? ngsf...@hygenomics.com ___ 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 install nginx
The order is not very important… however I would install nginx and postgres at the same time, then galaxy. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 1, 2014, at 10:10 AM, ngsf...@hygenomics.commailto:ngsf...@hygenomics.com wrote: dear sir: nginx postgress galaxy which one first install ? ngsf...@hygenomics.commailto:ngsf...@hygenomics.com ___ 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/
[galaxy-dev] Galaxy Security Vulnerability
A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python pickle functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability. Because this vulnerability allows for arbitrary code execution, administrators are strongly encouraged to apply this fix IMMEDIATELY. We have tried to make it as easy and quick as possible for server administrators to update their Galaxy instances. The fix has been applied to every stable release from 2013.01.13 until the tip, so it is possible to get this fix on older releases without updating to a newer feature release. You can do this by identifying your current release and updating to the `latest_release_date` tag corresponding to your release. For example, if you are running release_2013.11.04 (or a subsequent commit to the stable branch of Galaxy between release_2013.11.04 and release_2014.02.10), you can update with: % hg pull % hg update latest_2013.11.04 For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. If you do not want to pull any upstream changes, we have also created a standalone patch that fixes this problem, with multiple versions depending on your current Galaxy release: - pickle-2013.11.04.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.11.04 up to the current stable tip. Available at: https://depot.galaxyproject.org/patch/pickle-2013.11.04.patch - pickle-2013.01.13.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.01.13 up to 2013.08.12, and possibly older versions of Galaxy as well. Available at: https://depot.galaxyproject.org/patch/pickle-2013.01.13.patch If you happen to be running a very recent revision on the default branch or the newly created next-stable branch, a pickle-default.patch file exists at the same place. For older releases or instances with conflicting local modifications, manual application of the patch should not be difficult as it only includes a few small changes. To apply the patch, navigate to the root of your Galaxy directory, then run (replacing url_to_patch with the URL above that is correct for your release): % wget -O pickle.patch url_to_patch or: % curl -o pickle.patch url_to_patch and then: % patch -p1 pickle.patch patching file lib/galaxy/util/__init__.py Hunk #1 succeeded at 575 with fuzz 2 (offset -113 lines). patching file lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py Again, for the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. The Galaxy Team would like to extend special thanks to Inge Alexander Raknes and colleagues, who privately disclosed the vulnerability, with a full analysis and proof of concept. Credit for the fix and subsequent testing goes to my fellow Galaxy Team members John Chilton and Dannon Baker. On behalf of the Galaxy Team, --nate___ 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] galaxy won't start
Thanks for the fast reply! I tried it in the clean environment and it works.
I somehow totally missed that step when setting this up! So do I need to add
these 2 steps to my startup script?
/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env
. ./galaxy_env/bin/activate
Thanks,
Dori
-Original Message-
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Tuesday, July 29, 2014 10:00 AM
To: Sajdak, Doris
Cc: Galaxy Dev
Subject: 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] Galaxy error
Hello,
Thanks for the bug report. Is this on the main public server (usegalaxy.org)
or a local instance at the University of Iowa?
-John
On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A emily-b...@uiowa.edu
wrote:
Hello,
I have repeatedly gotten the following error message when attempting to
use both the mapping and pileup functions in Galaxy. I am using files that
I have previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user username emilybeck quota_percent 19 total_disk_usage 52086193970
nice_total_disk_usage 48.5 GB email emily-b...@uiowa.edu is_admin false
tags_usedmodel_class User id 03f0554e2314759esource
HDACollection(f313d1d65c4ee57e,451) 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 0status
500 statusText Internal Server Error responseHeaders Server nginx/1.4.7
Date Wed, 16 Jul 2014 15:19:52 GMT Content-Type application/json
Transfer-Encoding chunked Connection keep-alive Cache-Control
max-age=0,no-cache,no-store
options dataparse true emulateHTTP false emulateJSON false
*Emily Beck *PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
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Re: [galaxy-dev] [galaxy-iuc] writing datatypes
Hi Greg, thanks for the clarification. Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning bjo...@gruenings.eu wrote: Hi, single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and want to ship a X - Y converter (Y - X is also possible), we will end up with a dependency loop, or? The X repository will depend on the Y repository, but Y is depending on X, because we want to include a Y - X converter. Any idea how to solve that? I don't see a problem here, so I'm hoping I'm correctly understanding the issue. If we have: repo_x contains the single datatype X repo_y contains the single datatype Y repo_x_to_y_converter contains a tool that converts datatype X to datatype Y (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) repo_y_to_x_cenverter contains a tool that converts datatype Y to datatype X (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) Now if we want to install both the repo_x_to_y_converter and the repo_y_to_x_cenverter automatically whenever either one is installed, we have 2 options: 1) define a 3rd dependency relationshiop for repo_x_to_y_converter to depend on repo_y_to_x_cenverter and, similarly a 3rd dependency relationshiop for repo_y_to_x_cenverter on repo_x_to_y_converter. This does indeed create a circular repository dependency relationship, but the Tool Shed installation process will handle it correctly, installing all 4 repositories with proper dependency relationships created between them Does that mean, circular dependencies will be no problem at all? Do you consider including the converters into the datatypes as best-practise? (These converters are implicit-galaxy-converters). I would have only two repositories with circular dependencies. 2) Instead of creating a circlular dependency relationship between repo_x_to_y_converter and repo_y_to_x_cenverter, create an additional suite_definition_x_y repository (of type repository_suite_definition that defines relationships to repo_x_to_y_converter and repo_y_to_x_cenverter, ultimately installing all 4 repositories, but without defining any circular dependency relationships. repo_x_to_y_converter and repo_y_to_x_converter would have dependencies on datatype X and Y, so I do not see the need for a suite_definition ... or it is some collection like the emboss_datatypes ... My scenario is more that the converters are not tools, they are implicit converters and should _not_ be displayed in the tool panel. As far as I know they need to be defined inside the datatypes_conf.xml file. I think if circular dependencies are not a problem I will try to implement a proof of concept. EMBOSS is now splitted: https://github.com/bgruening/galaxytools/tree/master/datatypes/emboss_datatypes Thanks Greg! Bjoern Either of the above 2 scenarios will correctly install the 4 repositories. Let me know if I'm missing something here. Thanks! Greg Excellent example! How to handle versions of datatypes? Extra repositories for stockholm 1.0 and 1.1? If so ... the associated python file (sniffing, splitting ...) should be also versioned, or? What happend if I have two stockholm.py files in my system? Potentially you might need/want to define those as two different Galaxy datatypes? @Peter, can we create a striped-down, python only biopython egg? All parsers should be included, Bio.SeqIO should be sufficient I think. Right now, yes in principle (and this is fine from the licence point of view), but in practise this is a fair chunk of work. However, we are looking at this - see https://github.com/biopython/biopython/issues/349 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/ ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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-iuc] writing datatypes
Hi Björn, On Jul 22, 2014, at 6:01 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Greg, thanks for the clarification. Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning bjo...@gruenings.eu wrote: Hi, single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and want to ship a X - Y converter (Y - X is also possible), we will end up with a dependency loop, or? The X repository will depend on the Y repository, but Y is depending on X, because we want to include a Y - X converter. Any idea how to solve that? I don't see a problem here, so I'm hoping I'm correctly understanding the issue. If we have: repo_x contains the single datatype X repo_y contains the single datatype Y repo_x_to_y_converter contains a tool that converts datatype X to datatype Y (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) repo_y_to_x_cenverter contains a tool that converts datatype Y to datatype X (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) Now if we want to install both the repo_x_to_y_converter and the repo_y_to_x_cenverter automatically whenever either one is installed, we have 2 options: 1) define a 3rd dependency relationshiop for repo_x_to_y_converter to depend on repo_y_to_x_cenverter and, similarly a 3rd dependency relationshiop for repo_y_to_x_cenverter on repo_x_to_y_converter. This does indeed create a circular repository dependency relationship, but the Tool Shed installation process will handle it correctly, installing all 4 repositories with proper dependency relationships created between them Does that mean, circular dependencies will be no problem at all? Yes, the Tool Shed handles circular dependency definitions of any variety, so circular dependency definitions pose no problem. Do you consider including the converters into the datatypes as best-practise? (These converters are implicit-galaxy-converters). I would have only two repositories with circular dependencies. Yes, however, there are some current limitations in the framework detailed on this Trello card: https://trello.com/c/Ho3ra4b9/206-add-support-for-datatype-converters-and-display-applications Tag sets like the following that are defined in a datatypes_conf.xml file contained in a repository should be correctly loaded into the in-memory datatypes registry when the repository is instlled into Galaxy. However, it has been quite a while since I've worked in this area, so let me know if you encounter any issues. The current best practice is probaly that the converters themselved would each individually be in separate repositories (just like all Galaxy tools), but this can certainly be discussed if appropriate. Community thoughts are welcome here! datatype extension=bam type=galaxy.datatypes.binary:Bam mimetype=application/octet-stream display_in_upload=true converter file=bam_to_bai.xml target_datatype=bai/ converter file=bam_to_bigwig_converter.xml target_datatype=bigwig/ display file=ucsc/bam.xml / display file=ensembl/ensembl_bam.xml / display file=igv/bam.xml / display file=igb/bam.xml / /datatype 2) Instead of creating a circlular dependency relationship between repo_x_to_y_converter and repo_y_to_x_cenverter, create an additional suite_definition_x_y repository (of type repository_suite_definition that defines relationships to repo_x_to_y_converter and repo_y_to_x_cenverter, ultimately installing all 4 repositories, but without defining any circular dependency relationships. repo_x_to_y_converter and repo_y_to_x_converter would have dependencies on datatype X and Y, so I do not see the need for a suite_definition ... or it is some collection like the emboss_datatypes … I agree. My scenario is more that the converters are not tools, they are implicit converters and should _not_ be displayed in the tool panel. As far as I know they need to be defined inside the datatypes_conf.xml file. Yes, they must be defined inside the datatypes_conf.xml file. However, converters are just special Galaxy Tools (they are special in the same way that Data Manager tools are special). They are loaded into the in-memory Galaxy tools registry, but not displayed in the tool panel. I think if circular dependencies are not a problem I will try to implement a proof of concept. EMBOSS is now splitted: Sounds goos - circular dependencies should pose no problems. https://github.com/bgruening/galaxytools/tree/master/datatypes/emboss_datatypes Thanks Greg! Bjoern Either of the above 2 scenarios will correctly install the 4 repositories. Let me know if I'm missing something here. Thanks! Greg Excellent example! How to handle
Re: [galaxy-dev] [galaxy-iuc] writing datatypes
Before we go too much further down this path with dataytpes, I'm wondering if some of us should put together a spec of some kind that allows us to all agree on the direction. For example, I'm wondering if datatyps should be versioned and have a name-spaced identifier much like the Tool Shed's guid identifier for tools. I haven't thought too much about whether this would pose backward compatibility issues or not. Discussion is welcomed on this. Greg Von Kuster On Jul 22, 2014, at 7:19 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Björn, On Jul 22, 2014, at 6:01 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Greg, thanks for the clarification. Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning bjo...@gruenings.eu wrote: Hi, single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and want to ship a X - Y converter (Y - X is also possible), we will end up with a dependency loop, or? The X repository will depend on the Y repository, but Y is depending on X, because we want to include a Y - X converter. Any idea how to solve that? I don't see a problem here, so I'm hoping I'm correctly understanding the issue. If we have: repo_x contains the single datatype X repo_y contains the single datatype Y repo_x_to_y_converter contains a tool that converts datatype X to datatype Y (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) repo_y_to_x_cenverter contains a tool that converts datatype Y to datatype X (this repository also defines 2 dependency relationships, one to repo_x and another to repo_y) Now if we want to install both the repo_x_to_y_converter and the repo_y_to_x_cenverter automatically whenever either one is installed, we have 2 options: 1) define a 3rd dependency relationshiop for repo_x_to_y_converter to depend on repo_y_to_x_cenverter and, similarly a 3rd dependency relationshiop for repo_y_to_x_cenverter on repo_x_to_y_converter. This does indeed create a circular repository dependency relationship, but the Tool Shed installation process will handle it correctly, installing all 4 repositories with proper dependency relationships created between them Does that mean, circular dependencies will be no problem at all? Yes, the Tool Shed handles circular dependency definitions of any variety, so circular dependency definitions pose no problem. Do you consider including the converters into the datatypes as best-practise? (These converters are implicit-galaxy-converters). I would have only two repositories with circular dependencies. Yes, however, there are some current limitations in the framework detailed on this Trello card: https://trello.com/c/Ho3ra4b9/206-add-support-for-datatype-converters-and-display-applications Tag sets like the following that are defined in a datatypes_conf.xml file contained in a repository should be correctly loaded into the in-memory datatypes registry when the repository is instlled into Galaxy. However, it has been quite a while since I've worked in this area, so let me know if you encounter any issues. The current best practice is probaly that the converters themselved would each individually be in separate repositories (just like all Galaxy tools), but this can certainly be discussed if appropriate. Community thoughts are welcome here! datatype extension=bam type=galaxy.datatypes.binary:Bam mimetype=application/octet-stream display_in_upload=true converter file=bam_to_bai.xml target_datatype=bai/ converter file=bam_to_bigwig_converter.xml target_datatype=bigwig/ display file=ucsc/bam.xml / display file=ensembl/ensembl_bam.xml / display file=igv/bam.xml / display file=igb/bam.xml / /datatype 2) Instead of creating a circlular dependency relationship between repo_x_to_y_converter and repo_y_to_x_cenverter, create an additional suite_definition_x_y repository (of type repository_suite_definition that defines relationships to repo_x_to_y_converter and repo_y_to_x_cenverter, ultimately installing all 4 repositories, but without defining any circular dependency relationships. repo_x_to_y_converter and repo_y_to_x_converter would have dependencies on datatype X and Y, so I do not see the need for a suite_definition ... or it is some collection like the emboss_datatypes … I agree. My scenario is more that the converters are not tools, they are implicit converters and should _not_ be displayed in the tool panel. As far as I know they need to be defined inside the datatypes_conf.xml file. Yes, they must be defined inside the datatypes_conf.xml file. However, converters are just special Galaxy Tools (they are special in the same way that Data Manager tools are
[galaxy-dev] Galaxy+Toolshed Docker image?
I know there is a base docker image for Galaxy stable ( https://registry.hub.docker.com/u/bgruening/galaxy-stable/), but is there a docker image that will start both a server and a toolshed sever and link them? I was hoping that I could use something like that for testing shed based tool deployment. Kyle ___ 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+Toolshed Docker image?
Hi Kyle, not that I know of, but I'm interested in adding such a feature on top of the base galaxy image. You can find the Dockerfile here: https://github.com/bgruening/docker-recipes Ciao, Bjoern Am 21.07.2014 15:39, schrieb Kyle Ellrott: I know there is a base docker image for Galaxy stable ( https://registry.hub.docker.com/u/bgruening/galaxy-stable/), but is there a docker image that will start both a server and a toolshed sever and link them? I was hoping that I could use something like that for testing shed based tool deployment. Kyle ___ 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/
[galaxy-dev] Galaxy error
user
usernameemilybeck
quota_percent 19
total_disk_usage52086193970
nice_total_disk_usage 48.5 GB
email emily-b...@uiowa.edu
is_adminfalse
tags_used
model_class User
id 03f0554e2314759e
source HDACollection(f313d1d65c4ee57e,451)
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_code0
status 500
statusText Internal Server Error
responseHeaders
Server nginx/1.4.7
DateWed, 16 Jul 2014 15:19:52 GMT
Content-Typeapplication/json
Transfer-Encoding chunked
Connection keep-alive
Cache-Control max-age=0,no-cache,no-store
options
data
parse true
emulateHTTP false
emulateJSON false
Emily Beck
PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
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[galaxy-dev] Galaxy error
Hello,
I have repeatedly gotten the following error message when attempting to use
both the mapping and pileup functions in Galaxy. I am using files that I have
previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user
usernameemilybeck
quota_percent 19
total_disk_usage52086193970
nice_total_disk_usage 48.5 GB
email emily-b...@uiowa.edu
is_adminfalse
tags_used
model_class User
id 03f0554e2314759e
source HDACollection(f313d1d65c4ee57e,451)
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_code0
status 500
statusText Internal Server Error
responseHeaders
Server nginx/1.4.7
DateWed, 16 Jul 2014 15:19:52 GMT
Content-Typeapplication/json
Transfer-Encoding chunked
Connection keep-alive
Cache-Control max-age=0,no-cache,no-store
options
data
parse true
emulateHTTP false
emulateJSON false
Emily Beck
PhD Candidate
Llopart Lab
469 Biology Building
Iowa City, IA 52242
Lab: (319)335-3430
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[galaxy-dev] Galaxy/ODoSE - Output accessory orthologous genes ERROR
Dear Galaxy team, I am having a problem running Galaxy/ODoSE. In the step Extract categorize orthologs, I selected the option Output accessory orthologous genes but it didn't work and didn't output any file. The stdout contains multiple warnings: ... WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 11 in complete genomes table WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 10 in complete genomes table WARNING 15:18:06 select_taxa.select_genomes_by_ids:33 Could not find genome with BioProject ID 14 in complete genomes table WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead WARNING 15:18:08 __init__.get_most_recent_gene_name:186 Could not retrieve gene name annotation based on date; returning first gene name annotation instead ... How can I solve this problem? Thank you in advance! Best Regards, Sérgio ___ 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 mobile site
I hope this isn't a FAQ; I have not yet found the question (or answer) online, though I can't imagine I'm the first to ask: Are there plans to make a mobile version of the Galaxy website? Many of the biologists with whom I work would like to be able to monitor and start Galaxy jobs from their iPhones (or other smart phone). While it is possible to do so using the regular website, a mobile-specific site could make it easier. We searched in vain for an app, but I gather that would be a headache to maintain with such a dynamic website. A mobile site seems the right approach, unless there are good reasons not to try it? We may experiment with creating one for our own local Galaxy installation, but would prefer to use existing code if it's available. Many thanks, -- Dr. Mark Rogers Intelligent Systems Laboratory Department of Engineering Mathematics University of Bristol ___ 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 mobile site
Hi Mark There used to be a nice one: try adding '/mobile to your galaxy url. It is still kind of working (just without the graphics), and it is sufficient to monitor jobs. Hans-Rudolf There used to be one. On 06/26/2014 08:03 AM, MF Rogers wrote: I hope this isn't a FAQ; I have not yet found the question (or answer) online, though I can't imagine I'm the first to ask: Are there plans to make a mobile version of the Galaxy website? Many of the biologists with whom I work would like to be able to monitor and start Galaxy jobs from their iPhones (or other smart phone). While it is possible to do so using the regular website, a mobile-specific site could make it easier. We searched in vain for an app, but I gather that would be a headache to maintain with such a dynamic website. A mobile site seems the right approach, unless there are good reasons not to try it? We may experiment with creating one for our own local Galaxy installation, but would prefer to use existing code if it's available. Many thanks, -- Dr. Mark Rogers Intelligent Systems Laboratory Department of Engineering Mathematics University of Bristol ___ 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 mobile site
Thanks for the link -- easy enough, though a bit crude, if I may say so. If that's the only existing implementation then I think we'll look into making our own improvements, perhaps to share with the community. Assuming we have time, of course...! -- Dr. Mark Rogers Research Assistant Intelligent Systems Laboratory Department of Engineering Mathematics 0117 33 15328 On 26 June 2014 07:42, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Mark There used to be a nice one: try adding '/mobile to your galaxy url. It is still kind of working (just without the graphics), and it is sufficient to monitor jobs. Hans-Rudolf There used to be one. On 06/26/2014 08:03 AM, MF Rogers wrote: I hope this isn't a FAQ; I have not yet found the question (or answer) online, though I can't imagine I'm the first to ask: Are there plans to make a mobile version of the Galaxy website? Many of the biologists with whom I work would like to be able to monitor and start Galaxy jobs from their iPhones (or other smart phone). While it is possible to do so using the regular website, a mobile-specific site could make it easier. We searched in vain for an app, but I gather that would be a headache to maintain with such a dynamic website. A mobile site seems the right approach, unless there are good reasons not to try it? We may experiment with creating one for our own local Galaxy installation, but would prefer to use existing code if it's available. Many thanks, -- Dr. Mark Rogers Intelligent Systems Laboratory Department of Engineering Mathematics University of Bristol ___ 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/
[galaxy-dev] Galaxy Tool Wrapper/DTD/Schema Needed
Hi, I am working for USD Bioinformatics and trying to integrate Galaxy tools in an application. I have been looking at this site: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax? but was wondering if there was anyway to get the actual DTD or Schema for your tool definitions. Is this possible? Thanks, Tyler Jones ___ 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 Tool Wrapper/DTD/Schema Needed
Your question was answered in the negative on biostar a few days back: https://biostar.usegalaxy.org/p/8101/ Contributions welcomed. On Sat, Jun 21, 2014 at 8:25 AM, Jones, Tyler William tyler.jo...@coyotes.usd.edu wrote: Hi, I am working for USD Bioinformatics and trying to integrate Galaxy tools in an application. I have been looking at this site: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax but was wondering if there was anyway to get the actual DTD or Schema for your tool definitions. Is this possible? Thanks, Tyler Jones ___ 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-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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___
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Re: [galaxy-dev] Galaxy updated botched?
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/
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?
Thanks to everyone for their input. John, your explanation was excellent. I completely agree with the implementation of galaxy as it stands now (with a minor documentation warning about default mysql engine switch in v5.5). Personally, I either place trust in the ORM to maintain referential integrity or I offload it to the DB Engine. Hence, I will keep the MyISAM tables going for now after I do some validation against an InnoDB database (please no MyISAM engine hate-mail LOL). With respect to dropping MySQL support, I will let that one go by for now LOL. Thanks again for your contributions and maintenance of this great platform. I feel that it will be a game changer in the bioinformatics community. Regards, 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: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Thursday, June 12, 2014 9:16 AM To: Hans-Rudolf Hotz Cc: John Chilton; Kandalaft, Iyad; galaxy-...@bx.psu.edu Subject: 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.chmailto: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-dev Digest, Vol 96, Issue 14
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?
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 args to make every table an innodb engine table or do I add a new schema and modify all tables to use the innodb engine? Alternatively, I can use DDL events def after_create(target, connection, **kw): connection.execute(ALTER TABLE %s ENGINE=InnoDB; (target.name, target.name)) Thank you for your help. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.camailto:iyad.kandal...@agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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?
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 args to make every table an innodb engine table or do I add a new schema and modify all tables to use the innodb engine? Alternatively, I can use DDL events def after_create(target, connection, **kw): connection.execute(ALTER TABLE %s ENGINE=InnoDB; (target.name, target.name)) Thank you for your help. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue 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 Government of Canada | Gouvernement du Canada
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] Galaxy updated botched?
Dannon John, Thank you for your feedback. I agree that documentation is a good start. I’m still in the process of figuring out what actually happens to the database schema. It may be completely fine with no referential integrity constraints, which I’m okay with to some degree (we’re still in the infancy stages with Galaxy). I find it odd that these referential integrity errors popped up “all of a sudden” because I don’t recall noticing these errors when I first installed galaxy/initialized the database. I did move the database to the new version of MySQL, where InnoDB is the default and referencing primary keys on a MyISAM table caused the problem. As a side note, I would be interested to know your reasons for avoiding a hardcoded mysql engine. If galaxy depends on referential integrity (not that I am assuming it does), then setting the MySQL engine to Memory or MyISAM would be disastrous. Also, do you see any distinct advantages to using MyISAM for galaxy? Regards, 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: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Wednesday, June 11, 2014 10:23 AM To: John Chilton Cc: Kandalaft, Iyad; galaxy-...@bx.psu.edu Subject: 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.commailto: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.camailto: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.camailto:iyad.kandal...@agr.gc.ca Telephone | Téléphone 613-759-1228tel:613-759-1228 Facsimile | Télécopieur 613-759-1701tel:613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600tel:613-773-2600 Government of Canada | Gouvernement du Canada From: Kandalaft, Iyad Sent: Tuesday, June 10, 2014 1:39 PM
Re: [galaxy-dev] Galaxy updated botched?
On Wed, Jun 11, 2014 at 3:26 PM, Kandalaft, Iyad iyad.kandal...@agr.gc.ca wrote: Dannon John, Thank you for your feedback. I agree that documentation is a good start. I’m still in the process of figuring out what actually happens to the database schema. It may be completely fine with no referential integrity constraints, which I’m okay with to some degree (we’re still in the infancy stages with Galaxy). I find it odd that these referential integrity errors popped up “all of a sudden” because I don’t recall noticing these errors when I first installed galaxy/initialized the database. I did move the database to the new version of MySQL, where InnoDB is the default and referencing primary keys on a MyISAM table caused the problem. As a side note, I would be interested to know your reasons for avoiding a hardcoded mysql engine. If galaxy depends on referential integrity (not that I am assuming it does), then setting the MySQL engine to Memory or MyISAM would be disastrous. Also, do you see any distinct advantages to using MyISAM for galaxy? Well there have never been any reports of anyone having problems with MyISAM in particular - its the switch here that seems to be the problem as far as I can tell. If I had to venture a guess as to why no one has complained about non-InnoDB engines - I would say the referential integrity constraints are never violated by the statements that the ORM generates - so they are a nice to have backup primary protection - but are not strictly required. Certainly, if one has to use MySQL and has a choice I would recommend InnoDB for most interesting applications and Galaxy in particular, but *IF* we forced it we would break existing Galaxy installations using MyISAM right? If one did not have to worry about breaking Galaxy installations - I think a majority of the devteam would like drop support for MySQL entirely (and I think our recommendation of Postgres is unanimous). If anyone out there has tired using Galaxy with strictly MyISAM tables and found it untenable - by all means please chime in. -John Regards, 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: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Wednesday, June 11, 2014 10:23 AM To: John Chilton Cc: Kandalaft, Iyad; galaxy-...@bx.psu.edu Subject: 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
Re: [galaxy-dev] 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 args to make every table an innodb engine table or do I add a new schema and modify all tables to use the innodb engine? Alternatively, I can use DDL events def after_create(target, connection, **kw): connection.execute(ALTER TABLE %s ENGINE=InnoDB; (target.name, target.name)) Thank you for your help. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: iyad.kandal...@agr.gc.camailto:iyad.kandal...@agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ 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 updated botched?
Hi everyone I was looking to upgrade galaxy to the latest verison. I did the usual hg pull; hg update;. I start up galaxy, it fetches some eggs, and then it tells me that I need a DB schema update. Fine, I ran sh db_manage.sh upgrade. All I see is a list of stack traces similar to the following. I'm using mysql and all the tables that galaxy had created are running under the myisam engine Hence, no foreign key constraints allowed. Why did this happen and can I simply convert all my tables to InnoDB to complete the database upgrade? Should I restore the DB from a backup? IntegrityError: (IntegrityError) (1215, 'Cannot add foreign key constraint') '\nCREATE TABLE history_dataset_collection_rating_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\tuser_id INTEGER, \n\trating INTEGER, \n\tPRIMARY KEY (id), \n\tFOREIGN KEY(history_dataset_collection_id) REFERENCES history_dataset_collection_association (id), \n\tFOREIGN KEY(user_id) REFERENCES galaxy_user (id)\n)\n\n' () (IntegrityError) (1215, 'Cannot add foreign key constraint') '\nCREATE TABLE history_dataset_collection_tag_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\ttag_id INTEGER, \n\tuser_id INTEGER, \n\tuser_tname VARCHAR(255), \n\tvalue VARCHAR(255), \n\tuser_value VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN KEY(history_dataset_collection_id) REFERENCES history_dataset_collection_association (id), \n\tFOREIGN KEY(tag_id) REFERENCES tag (id), \n\tFOREIGN KEY(user_id) REFERENCES galaxy_user (id)\n)\n\n' () Creating history_dataset_collection_tag_association table failed: (IntegrityError) (1215, 'Cannot add foreign key constraint') '\nCREATE TABLE history_dataset_collection_tag_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT, \n\thistory_dataset_collection_id INTEGER, \n\ttag_id INTEGER, \n\tuser_id INTEGER, \n\tuser_tname VARCHAR(255), \n\tvalue VARCHAR(255), \n\tuser_value VARCHAR(255), \n\tPRIMARY KEY (id), \n\tFOREIGN KEY(history_dataset_collection_id) REFERENCES history_dataset_collection_association (id), \n\tFOREIGN KEY(tag_id) REFERENCES tag (id), \n\tFOREIGN KEY(user_id) REFERENCES galaxy_user (id)\n)\n\n' () Traceback (most recent call last): File lib/galaxy/model/migrate/versions/0120_dataset_collections.py, line 179, in __create table.create() File build/bdist.linux-x86_64/egg/sqlalchemy/schema.py, line 593, in create checkfirst=checkfirst) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1972, in _run_visitor **kwargs).traverse_single(element) File build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py, line 106, in traverse_single return meth(obj, **kw) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/ddl.py, line 86, in visit_table self.connection.execute(schema.CreateTable(table)) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1449, in execute params) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1542, in _execute_ddl compiled File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1698, in _execute_context context) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py, line 1691, in _execute_context context) File build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py, line 331, in do_execute cursor.execute(statement, parameters) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue Regards, Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science Technology Branch Agriculture Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 ___ 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 is not sourcing tool environment
Hi Isabelle,
can you show us the requirements section from your tool?
Also you need to have a symbolic link from
tool_dependency_dir/hhsuite/2.0.16/ ponting to
tool_dependency_dir/hhsuite/default/
In tool_dependency_dir/hhsuite/default/ should be the env.sh file. If
you have the correct requirements section in your tool it should work.
Good luck!
Bjoern
Am 04.06.2014 01:17, schrieb Isabelle Phan:
I am using env.sh to manage my tool dependencies:
# tool_dependency_dir/hhsuite/2.0.16/env.sh
export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default
export HHLIB=${HHPRED_DIR}/lib/hh
export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH
Galaxy is not sourcing it. I have to manually source it before I restart
Galaxy.
I am following Using the env.sh file and cannot get it to work. What am
I missing?
Any help greatly appreciated,
thanks,
Isabelle
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Re: [galaxy-dev] galaxy is not sourcing tool environment
aahh, that must be it, thanks Bjoern!
I have the symbolic link, but I did not have the 'requirements' section
correct.
thanks so much for your help,
Isabelle
On 6/5/14 9:27 AM, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Isabelle,
can you show us the requirements section from your tool?
Also you need to have a symbolic link from
tool_dependency_dir/hhsuite/2.0.16/ ponting to
tool_dependency_dir/hhsuite/default/
In tool_dependency_dir/hhsuite/default/ should be the env.sh file. If
you have the correct requirements section in your tool it should work.
Good luck!
Bjoern
Am 04.06.2014 01:17, schrieb Isabelle Phan:
I am using env.sh to manage my tool dependencies:
# tool_dependency_dir/hhsuite/2.0.16/env.sh
export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default
export HHLIB=${HHPRED_DIR}/lib/hh
export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH
Galaxy is not sourcing it. I have to manually source it before I restart
Galaxy.
I am following Using the env.sh file and cannot get it to work. What
am
I missing?
Any help greatly appreciated,
thanks,
Isabelle
___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] Galaxy reports crashing with the latest stable release
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/
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] Galaxy customized tool config file
Thanks Bj örn! for pointing the right issue card, I uplifted those. Vipin On Wed, Jun 4, 2014 at 12:45 PM, Bj örn Grüning bjoern.gruen...@gmail.com wrote: Hi Vipin, that is currently not possible but a high priority of the Galaxy deavteam. You can follow the status in several trello cards: https://trello.com/c/VizlCET9 https://trello.com/c/phMelslw Ciao, Bjoern Am 04.06.2014 18:33, schrieb Vipin TS: Sorry for re-posting! any suggestions to make an interactive tool page. Thanks you, Vipin On Tue, May 20, 2014 at 5:25 PM, Vipin TS vipin...@gmail.com wrote: Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org ___ 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/
[galaxy-dev] galaxy is not sourcing tool environment
I am using env.sh to manage my tool dependencies:
# tool_dependency_dir/hhsuite/2.0.16/env.sh
export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default
export HHLIB=${HHPRED_DIR}/lib/hh
export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH
Galaxy is not sourcing it. I have to manually source it before I restart
Galaxy.
I am following Using the env.sh file and cannot get it to work. What am
I missing?
Any help greatly appreciated,
thanks,
Isabelle
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[galaxy-dev] Galaxy queue
Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on queue and expected wait time. 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/
Re: [galaxy-dev] Galaxy queue
Hi Neil, Via the GUI, if you are logged in as an administrator (i.e. your email address is listed in universe_wsgi.ini) there is a an admin tab (top banner, starting analyze data etc). This includes an option to see the current jobs. Via the command line API? I'm not sure, never looked. Peter On Mon, May 26, 2014 at 6:59 AM, neil.burd...@csiro.au wrote: Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on queue and expected wait time. 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/
Re: [galaxy-dev] Galaxy queue
On 05/26/2014 10:00 AM, Peter Cock wrote: Hi Neil, Via the GUI, if you are logged in as an administrator (i.e. your email address is listed in universe_wsgi.ini) there is a an admin tab (top banner, starting analyze data etc). This includes an option to see the current jobs. Via the command line API? I'm not sure, never looked. connect to the PostgreSQL (or MySQL) database - prferably with a read-only user, and count the jobs with state new (ie grey) and running (ie yellow) in the job table. And based on the other information stored in the job table (eg 'tool_id'), you can make a guess on the expected wait time Regards, Hans-Rudolf Peter On Mon, May 26, 2014 at 6:59 AM, neil.burd...@csiro.au wrote: Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on queue and expected wait time. 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] Galaxy queue
Thanks a lot guys for the help. That's just what I needed. I'll have a look at the database table Neil From: Hans-Rudolf Hotz [h...@fmi.ch] Sent: Monday, May 26, 2014 6:23 PM To: Peter Cock; Burdett, Neil (CCI, Herston - RBWH) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy queue On 05/26/2014 10:00 AM, Peter Cock wrote: Hi Neil, Via the GUI, if you are logged in as an administrator (i.e. your email address is listed in universe_wsgi.ini) there is a an admin tab (top banner, starting analyze data etc). This includes an option to see the current jobs. Via the command line API? I'm not sure, never looked. connect to the PostgreSQL (or MySQL) database - prferably with a read-only user, and count the jobs with state new (ie grey) and running (ie yellow) in the job table. And based on the other information stored in the job table (eg 'tool_id'), you can make a guess on the expected wait time Regards, Hans-Rudolf Peter On Mon, May 26, 2014 at 6:59 AM, neil.burd...@csiro.au wrote: Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on queue and expected wait time. 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/
[galaxy-dev] Galaxy is not running
Hi,
I am new to Galaxy, so am probably doing something silly.
My jobs do not finish and sometimes do not start. Here is the error message:
Details
user
usernamewatterber
quota_percent3
total_disk_usage10295907343
nice_total_disk_usage9.6 GB
emailatter...@unlv.nevada.edu
is_adminfalse
tags_used
model_classUser
ide2b7da49063484ac
sourceHDACollection(d686c5fd139f68f1,190)
xhr
readyState4
responseText{err_msg: Uncaught exception in exposed API method:,
err_code: 0}
responseJSON
err_msgUncaught exception in exposed API method:
err_code0
status500
statusTextInternal Server Error
responseHeaders
Servernginx/1.4.7
DateThu, 22 May 2014 16:23:06 GMT
Content-Typeapplication/json
Transfer-Encodingchunked
Connectionkeep-alive
Cache-Controlmax-age=0,no-cache,no-store
options
data
parsetrue
emulateHTTPfalse
emulateJSONfalse
Any information would be awesome.
Thank you,
Wally
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[galaxy-dev] Galaxy customized tool config file
Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org ___ 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 on ubuntu 14.04: hangs on metadata cleanup
It seems to be an NFS related issue. When I run a separate VM as an NFS server that hosts the galaxy data (files, job workdir, tmp, ftp), problems are gone. There’s probably an explanation for that, but I’m going to leave it at this. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 07 May 2014, at 16:03, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: I should probably mention that the data filesystem is NFS, exported by the master from /mnt/galaxy/data and mounted on the worker. No separate fileserver. Master is the one that hangs. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 07 May 2014, at 15:57, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Dear all, Has anyone tried running Galaxy on Ubuntu 14.04? I’m trying a test setup on two virtual machines (worker+master) with a SLURM queue. Getting in strange problems when jobs finish, the master hangs, completely unresponsive with CPU at 100% (as reported by virt-manager, not by top). Only drmaa jobs seem to be affected. After hanging, a reboot shows the job is finished (and green in history). It took me some debugging to figure out where things go wrong, but it seems it goes wrong when os.remove is called in lib/galaxy/datatypes/metadata.py in method cleanup_external_metadata. I can reproduce the problem by calling os.remove(metadatafile) by hand (in an interactive python shell) when using pdb to create a breakpoint just before the call. If I comment out the os.remove it runs on until it hits another delete call in lib/galaxy/jobs/__init__.py: self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) It’s in the JobWrapper class in the cleanup() method. I should mention here that my galaxy version is a bit old since I’m running my own fork with local modifications on datatypes. This object_store.delete also leads to a shutil.rmtree and os.remove function. So, remove calls to the filesystem seem to hang the whole thing, but only at this point in time. Rebooting and removing by hand is no problem, pdb-stepping also sometimes fixes it (but if I just press continue it hangs). I don’t know where to go from here with debugging, but has anyone seen anything similar? Right now it feels like it may be caused by timing rather than actual code problems. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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 on ubuntu 14.04: hangs on metadata cleanup
Dear all, Has anyone tried running Galaxy on Ubuntu 14.04? I’m trying a test setup on two virtual machines (worker+master) with a SLURM queue. Getting in strange problems when jobs finish, the master hangs, completely unresponsive with CPU at 100% (as reported by virt-manager, not by top). Only drmaa jobs seem to be affected. After hanging, a reboot shows the job is finished (and green in history). It took me some debugging to figure out where things go wrong, but it seems it goes wrong when os.remove is called in lib/galaxy/datatypes/metadata.py in method cleanup_external_metadata. I can reproduce the problem by calling os.remove(metadatafile) by hand (in an interactive python shell) when using pdb to create a breakpoint just before the call. If I comment out the os.remove it runs on until it hits another delete call in lib/galaxy/jobs/__init__.py: self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) It’s in the JobWrapper class in the cleanup() method. I should mention here that my galaxy version is a bit old since I’m running my own fork with local modifications on datatypes. This object_store.delete also leads to a shutil.rmtree and os.remove function. So, remove calls to the filesystem seem to hang the whole thing, but only at this point in time. Rebooting and removing by hand is no problem, pdb-stepping also sometimes fixes it (but if I just press continue it hangs). I don’t know where to go from here with debugging, but has anyone seen anything similar? Right now it feels like it may be caused by timing rather than actual code problems. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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 on ubuntu 14.04: hangs on metadata cleanup
I should probably mention that the data filesystem is NFS, exported by the master from /mnt/galaxy/data and mounted on the worker. No separate fileserver. Master is the one that hangs. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 07 May 2014, at 15:57, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Dear all, Has anyone tried running Galaxy on Ubuntu 14.04? I’m trying a test setup on two virtual machines (worker+master) with a SLURM queue. Getting in strange problems when jobs finish, the master hangs, completely unresponsive with CPU at 100% (as reported by virt-manager, not by top). Only drmaa jobs seem to be affected. After hanging, a reboot shows the job is finished (and green in history). It took me some debugging to figure out where things go wrong, but it seems it goes wrong when os.remove is called in lib/galaxy/datatypes/metadata.py in method cleanup_external_metadata. I can reproduce the problem by calling os.remove(metadatafile) by hand (in an interactive python shell) when using pdb to create a breakpoint just before the call. If I comment out the os.remove it runs on until it hits another delete call in lib/galaxy/jobs/__init__.py: self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) It’s in the JobWrapper class in the cleanup() method. I should mention here that my galaxy version is a bit old since I’m running my own fork with local modifications on datatypes. This object_store.delete also leads to a shutil.rmtree and os.remove function. So, remove calls to the filesystem seem to hang the whole thing, but only at this point in time. Rebooting and removing by hand is no problem, pdb-stepping also sometimes fixes it (but if I just press continue it hangs). I don’t know where to go from here with debugging, but has anyone seen anything similar? Right now it feels like it may be caused by timing rather than actual code problems. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden ___ 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 REST API: multiple params per tool
The current method for supplying parameters to tools using the REST API for
workflows is fairly broken. The structure is as follow:
parameters:{
tool_1: {
param:param_name,
value:param value
},
tool_2: {
param:param_name,
value:param value
}
This structure means that it is impossible to submit more than 1 parameter
per tool within a workflow. Tools themselves, and workflows that use them,
have no problems with accepting multiple parameters. We should be
supporting something more like the following:
parameters:{
tool_1: {
param_name1:param value 1
param_name2:param value 2
},
tool_2: {
tool_2_param_name1:param value 1
tool_2_param_name2:param value 2
}
Is there any work towards something like this taking place? I imagine that
the REST API could support both formats (if the tool parameters dict has
anything in it other than param and value, use the new structure) for
backwards compatibility.
Thanks,
Jim
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Re: [galaxy-dev] Galaxy REST API: multiple params per tool
It looks like this is already the case, but only documented in the code
(lib/galaxy/webapps/galaxy/api/workflows.py):
def _update_step_parameters(step, param_map):
Update ``step`` parameters based on the user-provided ``param_map``
dict.
``param_map`` should be structured as follows::
PARAM_MAP = {STEP_ID: PARAM_DICT, ...}
PARAM_DICT = {NAME: VALUE, ...}
For backwards compatibility, the following (deprecated) format is
also supported for ``param_map``::
PARAM_MAP = {TOOL_ID: PARAM_DICT, ...}
in which case PARAM_DICT affects all steps with the given tool id.
If both by-tool-id and by-step-id specifications are used, the
latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also
be specified as::
PARAM_DICT = {'param': NAME, 'value': VALUE}
Note that this format allows only one parameter to be set per step.
Thanks,
Jim
On Mon, May 5, 2014 at 1:56 PM, Jim McCusker jmccus...@5amsolutions.comwrote:
The current method for supplying parameters to tools using the REST API
for workflows is fairly broken. The structure is as follow:
parameters:{
tool_1: {
param:param_name,
value:param value
},
tool_2: {
param:param_name,
value:param value
}
This structure means that it is impossible to submit more than 1 parameter
per tool within a workflow. Tools themselves, and workflows that use them,
have no problems with accepting multiple parameters. We should be
supporting something more like the following:
parameters:{
tool_1: {
param_name1:param value 1
param_name2:param value 2
},
tool_2: {
tool_2_param_name1:param value 1
tool_2_param_name2:param value 2
}
Is there any work towards something like this taking place? I imagine that
the REST API could support both formats (if the tool parameters dict has
anything in it other than param and value, use the new structure) for
backwards compatibility.
Thanks,
Jim
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Re: [galaxy-dev] Galaxy Error Message
I am running into a problem with coloring of my KEGG image produced. When loading pathview and running this script in R: pv.out-pathview(gene.data=gse16873.d, pathway.id=04110, species=hsa, out.suffix=gse) you get an image with full coloration. With the same command in galaxy, the image produced has only white and red, Im wondering if this is a problem within my scripts or what may be causing this: read-read.delim(file - gene.data, header=TRUE ) pv.out - pathview(gene.data=read, pathway.id= pathway.id, species=species, out.suffix=out.suffix, kegg.native=T) write.csv(pv.out$plot.data.gene, file=table) file.rename(paste(species, pathway.id, ., out.suffix, .png, sep = ), output) Thanks, Brad On Tue, Apr 29, 2014 at 6:30 PM, Ross ross.laza...@gmail.com wrote: FWIW: looks like a trivial xml syntax error is in this line: command interpreter=Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output /command .*..* There seem to be one too many - the first one is probably a problem? For the record, viewing your xml in firefox is sometimes very helpful for finding invalid xml which can otherwise be very hard to find. On Wed, Apr 30, 2014 at 2:32 AM, Bradley Belfiore bradbelf2...@gmail.comwrote: The XML file is: tool id=pathview name=pathview version=1.0 description Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs./description command interpreter=Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output /command inputs param name=gene.data type=data format=data label=enter input file/ param name=pathway.id type=text format=text label=Pathway ID/ param name=species type=text format=text label=Species/ param name=out.suffix type=text format=text label=Output Suffix / /inputs outputs data format=pdf name=output/ /outputs /tool With basic Rscript : args - commandArgs(TRUE) ## inputs gene.data - args[1] pathway.id - args[2] species -args[3] out.suffix -args[4] output -args[5] suppressMessages(library(pathview)) suppressMessages(library(KEGGgraph)) suppressMessages(library(Rgraphviz)) pv.out - pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T) On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Brad To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the command tag without defining it in a param tag. But it is difficult to guess without seeing to full xml file. Regards Hans-Rudolf On 04/29/2014 06:13 PM, Bradley Belfiore wrote: Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about: Traceback (most recent call last): File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py, line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py, line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'gene' On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-. I don't see the word Rscript_wrapper.sh in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id http://pathway.id http://pathway.id) : argument pathway.id http://pathway.id http://pathway.id is missing, with no default Calls: pathview
Re: [galaxy-dev] Galaxy Error Message
Thank you for your patience and help, I removed the periods and am running into this error: /bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: Permission denied Does it have to do with the fact Im using SQLite and not Postgres? On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Bradley, For your inputs, don’t use periods (‘.’) within the param names. Thanks for using Galaxy, Dan On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf2...@gmail.com wrote: The XML file is: tool id=pathview name=pathview version=1.0 description Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs./description command interpreter=Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output /command inputs param name=gene.data type=data format=data label=enter input file/ param name=pathway.id type=text format=text label=Pathway ID/ param name=species type=text format=text label=Species/ param name=out.suffix type=text format=text label=Output Suffix / /inputs outputs data format=pdf name=output/ /outputs /tool With basic Rscript : args - commandArgs(TRUE) ## inputs gene.data - args[1] pathway.id - args[2] species -args[3] out.suffix -args[4] output -args[5] suppressMessages(library(pathview)) suppressMessages(library(KEGGgraph)) suppressMessages(library(Rgraphviz)) pv.out - pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T) On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Brad To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the command tag without defining it in a param tag. But it is difficult to guess without seeing to full xml file. Regards Hans-Rudolf On 04/29/2014 06:13 PM, Bradley Belfiore wrote: Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about: Traceback (most recent call last): File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py, line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py, line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'gene' On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-. I don't see the word Rscript_wrapper.sh in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id http://pathway.id http://pathway.id) : argument pathway.id http://pathway.id http://pathway.id is missing, with no default Calls: pathview - grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes
Re: [galaxy-dev] Galaxy Error Message
Hi Bradley, For your inputs, don’t use periods (‘.’) within the param names. Thanks for using Galaxy, Dan On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf2...@gmail.com wrote: The XML file is: tool id=pathview name=pathview version=1.0 description Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs./description command interpreter=Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output /command inputs param name=gene.data type=data format=data label=enter input file/ param name=pathway.id type=text format=text label=Pathway ID/ param name=species type=text format=text label=Species/ param name=out.suffix type=text format=text label=Output Suffix / /inputs outputs data format=pdf name=output/ /outputs /tool With basic Rscript : args - commandArgs(TRUE) ## inputs gene.data - args[1] pathway.id - args[2] species -args[3] out.suffix -args[4] output -args[5] suppressMessages(library(pathview)) suppressMessages(library(KEGGgraph)) suppressMessages(library(Rgraphviz)) pv.out - pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T) On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Brad To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the command tag without defining it in a param tag. But it is difficult to guess without seeing to full xml file. Regards Hans-Rudolf On 04/29/2014 06:13 PM, Bradley Belfiore wrote: Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about: Traceback (most recent call last): File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py, line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py, line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'gene' On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-. I don't see the word Rscript_wrapper.sh in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id http://pathway.id http://pathway.id) : argument pathway.id http://pathway.id http://pathway.id is missing, with no default Calls: pathview - grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch mailto:h...@fmi.ch wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) :
Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?
Hi, I updated the test and the tool shed accordingly to Dave suggestion. I'm just wondering, the TS tests were passing with the old version, anything I should worry about? :) Thanks and sorry for the inconvenience! Bjoern Am 29.04.2014 16:07, schrieb Peter Cock: On Tue, Apr 29, 2014 at 2:59 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Based on the latest test run, and my own investigations, it would appear that the samtools compilation process is looking in the wrong include path for ncurses/ncurses_dll.h. My recommendation would be to replace the following: -I$NCURSES_INCLUDE_PATH/ncurses/ with -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH in the shell_command for package_samtools_0_1_19's tool_dependencies.xml that starts with: sed -i -e s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*| --Dave B. Thanks Dave, That sounds like it would be more robust to subtle server changes. I see Bjoern has been working on this today with a slightly different change - I'll leave this in his capable hands: https://github.com/bgruening/galaxytools/commits/master/orphan_tool_dependencies/package_samtools_0_1_19/tool_dependencies.xml Regards, 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/
Re: [galaxy-dev] Galaxy Error Message
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated. The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
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___
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Re: [galaxy-dev] Galaxy Error Message
Please keep all replies on the list by using reply all
well, what happens if you run
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running
as), replacing $genedata $pathwayid $species $output with meaningful
arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
command
interpreter=bashRscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
/command
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out now.
thanks,
Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in
the tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated. The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
_
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http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Galaxy Error Message
On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 04/28/2014 03:32 PM, Bradley Belfiore wrote: Thank you for your quick response, my command tag is: command interpreter=bashRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command So I believe Im calling R via the Rscript_wrapper.sh? There is a problem with the XML closing of the command tag. You appear to have a bash script calling an R script. Try: command interpreter=bashRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command Or, if you mark your shell script as executable and include the #!/bin/bash line, you don't need the interpreter setting: commandRscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output /command Also, you should be able to use relative paths rather than that absolute path (which is not portable). 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/
Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?
Hi Dave, This problem persists (or has reoccured), This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Did you discover anymore last week? Sorry for the lag in my reply, I busy with other things. Thanks, Peter On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation. --Dave B. On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote: Hi all, This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration? http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 Regards, Peter On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a new wrapper for samtools depad (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency (status Error) event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtoolspackage 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies/- installation of these additional repositories is required/ Tool shed NameOwner Changeset revision testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939 ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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 Error Message
The initial error now seems to be taken care of and now am getting this
message on attempting to run tool:
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 153, in prepare_job
job_wrapper.runner_command_line = self.build_command_line(
job_wrapper, include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs )
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 176, in build_command_line
return build_command( self, job_wrapper,
include_metadata=include_metadata,
include_work_dir_outputs=include_work_dir_outputs )
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py,
line 19, in build_command
commands_builder = CommandsBuilder(job_wrapper.get_command_line())
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py,
line 109, in __init__
commands = initial_command.rstrip(; )
AttributeError: 'NoneType' object has no attribute 'rstrip'
On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Please keep all replies on the list by using reply all
well, what happens if you run
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running as),
replacing $genedata $pathwayid $species $output with meaningful arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
command
interpreter=bashRscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
/command
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out
now.
thanks,
Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in
the tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R
script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore wrote:
I am new to galaxy and while trying to convert an R tool to a
Galaxy
usable tool I keep getting:
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax
error near unexpected token `('
/Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any help as to how to remedy this would be greatly appreciated.
The
first couple lines of my .R file are
#
#!/bin/bash
args-(commandArgs(TRUE))
Thanks,
Brad
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Re: [galaxy-dev] Galaxy Error Message
Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch - tryCatchList - tryCatchOne - Anonymous In addition: Warning message: In file(file, rt) : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On 04/28/2014 03:58 PM, Bradley Belfiore wrote: The initial error now seems to be taken care of and now am getting this message on attempting to run tool: File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 109, in __init__ commands = initial_command.rstrip(; ) AttributeError: 'NoneType' object has no attribute 'rstrip' This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. 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/
Re: [galaxy-dev] Galaxy Error Message
So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA' Error in grep(species, pathway.id) : argument pathway.id is missing, with no default Calls: pathview - grep Execution halted On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch - tryCatchList - tryCatchOne - Anonymous In addition: Warning message: In file(file, rt) : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: On 04/28/2014 03:58 PM, Bradley Belfiore wrote: The initial error now seems to be taken care of and now am getting this message on attempting to run tool: File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py, line 109, in __init__ commands = initial_command.rstrip(; ) AttributeError: 'NoneType' object has no attribute 'rstrip' This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. 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/
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
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[galaxy-dev] Galaxy/Cloudman Compute Nodes User
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/
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] Galaxy - Cloudman
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
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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:
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Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?
Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation. --Dave B. On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote: Hi all, This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration? http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 Regards, Peter On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a new wrapper for samtools depad (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency (status Error) event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtoolspackage 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies/- installation of these additional repositories is required/ Tool shed NameOwner Changeset revision testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939 ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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-iuc] Test ToolShed package_samtools_0_1_19 status error?
Thanks Dave, On a slight tangent, is there a way in the ToolShed to see what other repositories use a given repository as a dependency? e.g. From http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 it there any way to see what uses samtools 0.1.19? Cheers, Peter On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools installation. --Dave B. On Mon 21 Apr 2014 06:52:50 AM EDT, Peter Cock wrote: Hi all, This samtools dependency error is now showing for all my Test ToolShed repositories using the samtools package: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Looking at the package itself, it looks like a ncurses (or curses) library dependency problem - perhaps something changed on the ToolShed server configuration? http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 Regards, Peter On Wed, Apr 16, 2014 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com mailto:p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a new wrapper for samtools depad (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency (status Error) event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:* 13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtoolspackage 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies/- installation of these additional repositories is required/ Tool shed NameOwner Changeset revision testtoolshed.g2.bx.psu.edu http://testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939 ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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/
