[galaxy-dev] Login problem.
Dear Galaxy development team, I've got a problem using the login function of Galaxy. So I downloaded a copy of Galaxy distribution and installed it on a local machine, then I installed PostgreSQL on this machine and made the necessary changes to the universe_wsgi.ini file and Galaxy is able to the use the PostgreSQL database to store information. I was able to register a user account and then I could login to the system for the first time, but after I logout and login again, the system always says that I am logged out. I checked the log file of Postgresql and the log file of Galaxy system, there is no error message indicating what happened at all. I restarted Postgresql database and Galaxy system and then I was able to login, but after I logged out, I can not login again! Have you guys met this kind of problem before? Any suggestions on what could be the cause of this problem? Thanks so much! Luobin ___ 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/
Re: [galaxy-dev] SGE and Galaxy (a different approach)
Use qrsh instead of qsub to submit the job should help, I believe. On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart andrew.c.stew...@gmail.comwrote: I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different. Because I only want certain processes to be submitted to the queue, I'd rather control this at the tool configuration level (the xml wrapper). For example: command interpreter=bash qsub myscript.sh /command This will work, except that the status of the job (in Galaxy) shows as completed even though the job has simply been submitted to SGE. Basically Galaxy 'loses track' of the process because the submission process (myscript.sh) has completed even if the actual job hasn't. Has anyone else tried anything like this before, or have anything helpful to suggest? One thought is to somehow cause the myscript.sh process to pause until the SGE job has completed... somehow. Any advice appreciated. Thanks, Andrew ___ 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/ ___ 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/
[galaxy-dev] new data type.
Hi, I created an XML file for a tool. This tool has an Nexus input. When I click the input field of the web interface for this tool, it shows all kinds of data that I can select. How do I restrict the list to show only data in nexus format? I added a line in the registration part and the sniffer part of the datatypes_conf.xml and I also created a class called Nexus which inherits the class galaxy.datatypes.Sequence, but this doesn't solve the problem. Thanks, Luobin ___ 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/
Re: [galaxy-dev] Cluster setup - shared temporary directory
I benchmarked MrBayes 3.1.2 program on my cluster for two cases: 1. use local /tmp for temporary files 2. use the network shared /home/galaxy/galaxy-dist/database/tmp MrBayes is about 10 times slower for case 2 than for case 1. What I did was to set the network shared folder as the default but in the MrBayes wrapper, I changed the environment variable TEMP to be a local folder. Luobin On Tue, Jul 26, 2011 at 10:39 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Tue, Jul 26, 2011 at 5:16 PM, Duddy, John jdu...@illumina.com wrote: I can give you a very good example - if you are doing alignment and for some reason need to convert the input file before operating on them, such that you need a complete copy, /tmp may not have enough room. I have had this happen to me running lots of instances of an aligner, temporarily using 100G+ of temp space. I don't see the need to have a shared temp space, but I do see the need to be able to tell the tools where you want them to put temp files. So in your setup, the cluster nodes are not likely to have 100G+ on /tmp (i.e. the local hard drive of the node), so you want them to use a temp folder on the cluster shared storage? I think needs will differ between tools - in some cases you really want a fast local drive for temp files, and putting them on a network drive will just kill performance. Using /tmp seems a safe default. Is there any guidance for tool authors on where to put temp files, and how to access any related Galaxy settings? There is nothing currently listed here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax 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/ ___ 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/
Re: [galaxy-dev] [galaxy-user] scramble pbs_python egg
Hi, Nate, Yeah, I've already solved the issue, basically used the -e parameter as you mentioned here. I think the documentation should be corrected. Thanks, Luobin On Tue, Aug 16, 2011 at 12:53 PM, Nate Coraor n...@bx.psu.edu wrote: Luobin Yang wrote: Hi, I am trying to scramble the pbs_python egg for my galaxy installation, when I execute the following command: LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py pbs_python I got lots messages like the following: scramble(): Egg already exists, remove to force rebuild: /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-i686-ucs4.egg . but there is message about pbs_python and there is no pbs_python.egg generated in the eggs directory Hi Luobin, I've moved this discussion to the galaxy-dev list since it concerns a local installation. Sorry for the delay in response, if you've already resolved this issue please let us know. If not, please try the following: LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py -e pbs_python And paste the full output here if it fails. Thanks, --nate Anything wrong? Thanks, Luobin ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] ProFTPd on Ubuntu system.
Hi, Has anyone set up ProFTPd successfully on Ubuntu 10.04 to enable FTP upload on Galaxy? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. Thanks, Luobin ___ 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/
Re: [galaxy-dev] ProFTPd on Ubuntu system.
Hi, Enis, Thanks for sharing your method! I did some searching last night and figured out why the default proftpd package for Ubuntu 10.04 doesn't work; it doesn't come with a module that's needed for Galaxy: the mod_sql_passwd module. So I reinstalled proftpd from source and now it works fine :) Thanks again, Luobin On Tue, Sep 13, 2011 at 2:14 AM, Enis Afgan eaf...@emory.edu wrote: I forgot to mention earlier that you'll still need to do the database GRANT etc. as described on the wiki page you pointed to. The mentioned method does not do that. Enis On Tue, Sep 13, 2011 at 8:10 AM, Enis Afgan eaf...@emory.edu wrote: You can try extracting the ProFTP install method from mi-deployment and running only it via Fabric? We use this method to install ProFTP on the cloud and galaxy VM, both of which are based on Ubuntu 10.04. The method is available here: https://bitbucket.org/afgane/mi-deployment/src/d894af37a83b/mi_fabfile.py#cl-442 (also take a look at the _required_packages method and _setup_users method because some additional configuration is done there). Hope this helps, Enis On Mon, Sep 12, 2011 at 8:05 PM, Luobin Yang yangl...@isu.edu wrote: Hi, Has anyone set up ProFTPd successfully on Ubuntu 10.04 to enable FTP upload on Galaxy? I followed the instructions on this link ( http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't work. Thanks, Luobin ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy fronting multiple clusters
I have never setup a Galaxy instance fronting multiple clusters, but it's something I would like to explore. I have a dedicated cluster to run Galaxy jobs and I've got another a shared cluster to which I hope Galaxy can assign jobs when the dedicated cluster is too busy. From my understanding of Galaxy, the tool runner for each tool is hardcoded in the universe.ini file and if you do not configure a tool runner for a tool, Galaxy will use the default tool runner, which is determined by the default_cluster_job_runner parameter. I believe you can configure multiple job runners for a specific tool under the [galaxy:tool_runners] in universe.ini, for instance, for each cluster, you have a different tool runner for a specific tool, however, Galaxy probably will just use one of them, most likely the last one. So cluster selection for a tool is determined by the job runner, which is hard coded in the universe.ini file. As a result, the running of a workflow is determined by the tools in the workflow. If each tool in the workflow is configured to use the same cluster, then the workflow is run on the same cluster, otherwise, it will span multiple clusters. I think if you can configure the machine that runs Galaxy instance to be the submit host of multiple clusters, then it's possible to have Galaxy front multiple clusters. For me, the biggest hurdle is how to let two clusters having a shared storage space and configure a machine in one cluster to be the submit host of another cluster. Thanks, Luoin On Mon, Sep 19, 2011 at 9:44 AM, Ann Black annbl...@eng.uiowa.edu wrote: Hello - I am working on standing up our own galaxy installation. We would like to have galaxy front multiple clusters, and I have some questions I was hoping someone could help with. 1) From reading other forum posts on this subject, it seems I need to minimally do the following ... is this correct?: A) have galaxy server w/ sge register as a job submitting host to the head node of each cluster B) Configure multiple tool runners for each tool per remote cluster? 2) When galaxy would submit a job, how would a backend remote cluster be selected? When running workflows, would the same cluster be used to run the entire workflow - or could the workflow then span remote clusters? 3) I am trying to understand some of the source code, where is the logic that would then dispatch the job and select a job runner to use? 4) Other advice or steps needed in order to get galaxy to front multiple remote clusters? Thanks so much, Ann ___ 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/ ___ 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/
[galaxy-dev] What's causing this error?
Hi, Recently I moved my locally installed Galaxy from a local hard drive to an NFS mounted hard drive, when I run some tools, I go the following error from the log file: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. I am pretty sure the job was not manually dequeued. Any idea how this happened and how this can be fixed? Thanks, Luobin ___ 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/
Re: [galaxy-dev] What's causing this error?
Well, I didn't move it to a grid configuration using PBS recently, it was already using a grid configuration with PBS before I moved it to the NFS volume and no such an error ever happened :) So it must be related to NFS. Thanks for you great suggestions! I will try them out and see how they work on my system. Thanks, Luobin On Mon, Oct 17, 2011 at 12:45 PM, Duddy, John jdu...@illumina.com wrote: You mention that you moved it to an NFS volume – but it seems you also moved to a grid configuration using PBS? ** ** If that’s the case, what you are seeing might be an issue with NFS attribute caching or write caching, which causes files created from one machine to not appear until some time later (from the perspective of other machines). The PBS job notifications are not impacted by the filesystem latencies. ** ** You can prove this by experiment if you alter the finish_job method in lib/galaxy/jobs/runners/pbs.py to do a sleep/wait loop, waiting up to 60 seconds for the files to be readable. If that hack works, latency is your problem. ** ** The solution is either to: **- **Configure your mounts not to use attribute caching (has performance impacts), or **- **Make the hack permanent. ** ** This happened to us on SGE, which is why I know these details ;-} ** ** *John Duddy Sr. Staff Software Engineer Illumina, Inc. *9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com ** ** *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Luobin Yang *Sent:* Monday, October 17, 2011 10:31 AM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* [galaxy-dev] What's causing this error? ** ** Hi, ** ** Recently I moved my locally installed Galaxy from a local hard drive to an NFS mounted hard drive, when I run some tools, I go the following error from the log file: ** ** Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. ** ** I am pretty sure the job was not manually dequeued. Any idea how this happened and how this can be fixed? ** ** Thanks, Luobin ** ** ___ 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/
[galaxy-dev] transferring sample datasets stuck in 'In queue' status
Hi all, I configured Sample Tracking System in Galaxy to transfer datasets from a sequencer to data libraries, however, after I selected the datasets to be transferred on the sequencer and clicked Transfer button, the transfer status has been in queue forever. I didn't find any error message in galaxy_listener.log, however, I found the following error message in data_transfer.log: 2012-02-16 19:39:01,221 - datatx_3623 - Error. !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title405 Method Not Allowed/title /headbody h1Method Not Allowed/h1 pThe requested method PUT is not allowed for the URL /api/samples/1e8ab44153008be8./p hr addressApache/2.2.14 (Ubuntu) Server at xxx.xxx.xxx.xxx Port 80/address /body/html Any idea what went wrong? Thanks, Luobin ___ 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/
Re: [galaxy-dev] transferring sample datasets stuck in 'In queue' status
So I stopped using Apache as a proxy web server and use Galaxy as the web server directly. This time the status of the sample data transfer changed to Complete. So I believe Apache needs configuration modifications for this case, maybe Apache needs mod_dav module and other related modules? However, when I go to the data library where the datasets are supposed to go, there is no datasets in it, even though the sample sequence files have been transferred from the sequencer to the folder specified by library_import_dir in universe_wsgi.ini. They are just not imported to the data libraries automatically. When I looked at the data_transfer.log, I found the following error message: 2012-02-17 09:28:37,927 - datatx_7318 - 400 Bad Request The server could not comply with the request since it is either malformed or otherwise incorrect. Malformed LibraryFolder id ( 994debf9f6ab02b9912262b0bd04c784 ) specified, unable to decode 2012-02-17 09:28:37,928 - datatx_7318 - Setting status Complete for dataset All of sample 17 Luobin On Thu, Feb 16, 2012 at 7:58 PM, Luobin Yang yangl...@isu.edu wrote: Hi all, I configured Sample Tracking System in Galaxy to transfer datasets from a sequencer to data libraries, however, after I selected the datasets to be transferred on the sequencer and clicked Transfer button, the transfer status has been in queue forever. I didn't find any error message in galaxy_listener.log, however, I found the following error message in data_transfer.log: 2012-02-16 19:39:01,221 - datatx_3623 - Error. !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title405 Method Not Allowed/title /headbody h1Method Not Allowed/h1 pThe requested method PUT is not allowed for the URL /api/samples/1e8ab44153008be8./p hr addressApache/2.2.14 (Ubuntu) Server at xxx.xxx.xxx.xxx Port 80/address /body/html Any idea what went wrong? Thanks, Luobin ___ 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/
[galaxy-dev] Update on Megablast?
Hi, all, Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy? Thanks, Luobin ___ 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/
Re: [galaxy-dev] Update on Megablast?
Yeah, that's what I was wondering: to update megablast tool to use NCBI BLAST+ . I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI BLAST+, but it seems the output format is not compatible with the tool (Fetch taxonomic representation) in metagenomic analyses anymore. So it looks like the only solution at the moment is to have both NCBI NCBI+ and an old version of BLAST. Thanks, Luobin On Fri, Mar 23, 2012 at 10:55 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang yangl...@isu.edu wrote: I've noticed these wrappers for BLAST+. I actually was talking about the megablast tool under NGS Mapping section... Thanks, Luobin Oh - you mean update it to use BLAST+ instead of legacy BLAST internally? I asked about this too before writing the BLAST+ wrappers and one major concern was about breaking reproducibility - the newer BLAST doesn't give identical results. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003342.html Also everything the megablast wrapper offers and more is in the blastn wrapper. 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/
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f', u'
http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample status
from in queue to complete but didn't add the downloaded files to the data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406): python
/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messaging/server/data_transfer.py
data_transfer
galaxy_hostrd-galaxydev.app.pmi/galaxy_host
api_key69bbd1a9b18eda2a888e9963820d8ef0/api_key
data_hostchp723/data_host
data_usergalaxy/data_user
data_passwordmypassword/data_password
request_id12/request_id
sample_id12/sample_id
library_id15/library_id
folder_id52/folder_iddataset
dataset_id10/dataset_id
namettt_2.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz/file
/datasetdataset
dataset_id9/dataset_id
namettt_1.fastq.gz/name
file/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz/file
/dataset/data_transfer
universe_wsgi.ini
The FASTQ files are for testing and aren't very big (7.6 MB), what
could be going wrong?
regards,
Leandro
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[galaxy-dev] Error starting Galaxy after upgrade.
Hi, I upgraded Galaxy to the latest version using the command: hg pull -u, then when I run sh run.sh I got the following error messages: Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /usr/lib/python2.6/dist-packages/pkg_resources.py, line 546, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: mercurial==2.1.2 Fetch failed. What happened here? Thanks, Luobin ___ 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/
[galaxy-dev] tool shed data type problem?
Hi, After I update galaxy-dist to the latest version, I got the following error message when I run run.sh command: galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-01 09:57:15,503 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 64, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File /home/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py, line 26, in load_proprietary_datatypes load_datatype_items( self.app, tool_shed_repository, relative_install_dir ) File /home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py, line 1024, in load_datatype_items converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) File /home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py, line 236, in alter_config_and_load_prorietary_datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) TypeError: load_datatypes() got an unexpected keyword argument 'override' ___ 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/
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Hi, Greg,
I've still got issues after I downloaded the latest version from the dist
repository. So after I selected the datasets that I would like to transfer
from the sequencer and click the Transfer button, Galaxy generates an
error message : Invalid sample id (None)... I tried to delete this
dataset using the manage datasets menu, and Galaxy generates the same
error message: Invalid sample id (None). It seems galaxy system generates
the sample id automatically (the first one is sample_1), not sure why this
happens...
Luobin
On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Emily,
This issue should be resolved in change set 6924:12b14f3e78e9, which is
currently only available from our central repository. It will not be
available in the dist repository fro some time, so you'll have to pull it
from Galaxy central (https://bitbucket.org/galaxy/galaxy-central) if you
want it now.
Thanks very much for reporting this problem, and we apologize for the
inconvenience it caused.
Greg Von Kuster
On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
Hi Leandro,
I am also experiencing the same problem with the latest version of
galaxy. I just attempted to connect our sequencer for the first time
yesterday. I do not have an older version of galaxy to test and compare to
see if it works in earlier versions. I am able to transfer data from the
sequence to the import directory, however it is not moved to the data
library. My data_transfer.log also has the same error.
The server could not comply with the request since it is either
malformed or otherwise incorrect.
Does anyone have a solution for this?
Thanks
Emily
--
Message: 17
Date: Wed, 28 Mar 2012 13:15:47 +0200
From: Leandro Hermida soft...@leandrohermida.com
To: Luobin Yang yangl...@isu.edu
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in
queue forever
Message-ID:
caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Dear Galaxy Dev,
Ok I have gotten further found out what was going on, in my
data_transfer.log I was getting HTTP 404 Not Authorized when the data
transfer was trying to access Galaxy API URLs
http://galaxyserver/api/... This is because we are using external user
authentication as documented in
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
all of Galaxy behind this authentication. Since the Galaxy API uses
API keys to essentially authenticate you have to change you Location
/ ... /Location container to not match URLs starting with /api. To
do this you have to change it to LocationMatch ^/(?!api)
/LocationMatch.
best,
leandro
On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote:
I've got the same problem and when I looked at the data_transfer.log, I
saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f',
u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
'new_status': 'Adding to data library'})
2012-03-01 15:12:27,342 - datatx_13870 - Error. !DOCTYPE HTML PUBLIC
-//IETF//DTD HTML 2.0//EN
htmlhead
title405 Method Not Allowed/title
/headbody
h1Method Not Allowed/h1
pThe requested method PUT is not allowed for the URL
/api/samples/2d9035b3fc152403./p
hr
Using Galaxy instead of Apache as the web server changed the sample
status
from in queue to complete but didn't add the downloaded files to the
data
library.
Luobin
On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Dear Galaxy Dev,
I've set up the Galaxy sample tracking system data transfer
functionality exactly as specified here
https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
attempt to transfer datasets it puts them into the queue and then
never seems to transfer anything.
The galaxy_listener.log shows:
2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
{'config_file': 'universe_wsgi.ini', 'http_server_section':
'server:main'}
2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange': 'galaxy_exchange',
'rabbitmqctl_path':
'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rabbitmqctl',
'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
'5672'}
2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server -
127.0.0.1:5672
2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
2012-03-26 17:31:23,401
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Hi, Greg, Unfortunately I won't be able to attend these two conference. I spent a bit time looking at the codes that are related to the issue and I found why this issue is happening, even though I am not sure how this happened. Basically this happens on line 755 of requests_admin.py, which is this statement: sample_id = params.get( 'sample_id', None ) It seems this statement is executed twice for each dataset operation. For the first time of execution, sample_id contains the right ID but for the second time, sample_id contains None. Based on this observation, I have come up with a quick fix : I just added the following two lines after above line: if sample_id == None: sample_id = params.get( 'id', None ) This fixed the problem and I am able to transfer, delete, or rename sample datasets even though it doesn't eliminate the source that causes sample_id to have a value of None. Another small issue is that I can only transfer one dataset at a time. If I select two datasets and then click Transfer button, the system shows an error message of invalid sample_id, and the value of sample_id is actually a tuple instead of a single sample_id. I am not very sure if this is because the system is designed to handle just one dataset at a time or it's a bug in the code. Best, Luobin On Wed, Jul 11, 2012 at 8:54 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Luobin, I'm on my way to ISMB for a week, and then will be at the Galaxy Community Conference the following week, so I won't have time to help you track this problem down until some time in August unless you will be at either of these 2 conferences. Sorry for the inconvenience on this, but my schedule over the next few weeks is very hectic. If you'll be at either ISMB or the GCC, we can certainly get together to look at this. Greg Von Kuster On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote: Hi, Greg, I've still got issues after I downloaded the latest version from the dist repository. So after I selected the datasets that I would like to transfer from the sequencer and click the Transfer button, Galaxy generates an error message : Invalid sample id (None)... I tried to delete this dataset using the manage datasets menu, and Galaxy generates the same error message: Invalid sample id (None). It seems galaxy system generates the sample id automatically (the first one is sample_1), not sure why this happens... Luobin On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Emily, This issue should be resolved in change set 6924:12b14f3e78e9, which is currently only available from our central repository. It will not be available in the dist repository fro some time, so you'll have to pull it from Galaxy central (https://bitbucket.org/galaxy/galaxy-central) if you want it now. Thanks very much for reporting this problem, and we apologize for the inconvenience it caused. Greg Von Kuster On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: Hi Leandro, I am also experiencing the same problem with the latest version of galaxy. I just attempted to connect our sequencer for the first time yesterday. I do not have an older version of galaxy to test and compare to see if it works in earlier versions. I am able to transfer data from the sequence to the import directory, however it is not moved to the data library. My data_transfer.log also has the same error. The server could not comply with the request since it is either malformed or otherwise incorrect. Does anyone have a solution for this? Thanks Emily -- Message: 17 Date: Wed, 28 Mar 2012 13:15:47 +0200 From: Leandro Hermida soft...@leandrohermida.com To: Luobin Yang yangl...@isu.edu Cc: Galaxy Dev galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever Message-ID: caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Galaxy Dev, Ok I have gotten further found out what was going on, in my data_transfer.log I was getting HTTP 404 Not Authorized when the data transfer was trying to access Galaxy API URLs http://galaxyserver/api/. http://galaxyserver/api/.. This is because we are using external user authentication as documented in http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts all of Galaxy behind this authentication. Since the Galaxy API uses API keys to essentially authenticate you have to change you Location / ... /Location container to not match URLs starting with /api. To do this you have to change it to LocationMatch ^/(?!api) /LocationMatch. best, leandro On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang yangl...@isu.edu wrote: I've got the same problem and when I looked at the data_transfer.log, I saw the following message: 2012-03-01 15:12:27,338
Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever
Hi, Greg, I tested your fix in changeset 7388:28b3364341b6, it works fine on my local copy of Galaxy. I am able to transfer, delete, and rename sample datasets without any error message. Thanks, Luobin On Fri, Jul 13, 2012 at 8:19 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Luobin, Your information really helped narrow down the problem, and I've committed what I believe is a fix in change set 7388:28b3364341b6, which is currently available in the Galaxy central repository. This fix should be available in the next Galaxy dist update, which should be available soon. I am not able to fully test this fix though, so if you can let me know if problems still exist when you get a chance to test it, I'll look further into the problem after the GCC. Sorry for the inconvenience this has caused. Thanks ver much! Greg Von Kuster On Jul 12, 2012, at 1:07 PM, Luobin Yang wrote: Hi, Greg, Unfortunately I won't be able to attend these two conference. I spent a bit time looking at the codes that are related to the issue and I found why this issue is happening, even though I am not sure how this happened. Basically this happens on line 755 of requests_admin.py, which is this statement: sample_id = params.get( 'sample_id', None ) It seems this statement is executed twice for each dataset operation. For the first time of execution, sample_id contains the right ID but for the second time, sample_id contains None. Based on this observation, I have come up with a quick fix : I just added the following two lines after above line: if sample_id == None: sample_id = params.get( 'id', None ) This fixed the problem and I am able to transfer, delete, or rename sample datasets even though it doesn't eliminate the source that causes sample_id to have a value of None. Another small issue is that I can only transfer one dataset at a time. If I select two datasets and then click Transfer button, the system shows an error message of invalid sample_id, and the value of sample_id is actually a tuple instead of a single sample_id. I am not very sure if this is because the system is designed to handle just one dataset at a time or it's a bug in the code. Best, Luobin On Wed, Jul 11, 2012 at 8:54 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Luobin, I'm on my way to ISMB for a week, and then will be at the Galaxy Community Conference the following week, so I won't have time to help you track this problem down until some time in August unless you will be at either of these 2 conferences. Sorry for the inconvenience on this, but my schedule over the next few weeks is very hectic. If you'll be at either ISMB or the GCC, we can certainly get together to look at this. Greg Von Kuster On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote: Hi, Greg, I've still got issues after I downloaded the latest version from the dist repository. So after I selected the datasets that I would like to transfer from the sequencer and click the Transfer button, Galaxy generates an error message : Invalid sample id (None)... I tried to delete this dataset using the manage datasets menu, and Galaxy generates the same error message: Invalid sample id (None). It seems galaxy system generates the sample id automatically (the first one is sample_1), not sure why this happens... Luobin On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Emily, This issue should be resolved in change set 6924:12b14f3e78e9, which is currently only available from our central repository. It will not be available in the dist repository fro some time, so you'll have to pull it from Galaxy central (https://bitbucket.org/galaxy/galaxy-central) if you want it now. Thanks very much for reporting this problem, and we apologize for the inconvenience it caused. Greg Von Kuster On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote: Hi Leandro, I am also experiencing the same problem with the latest version of galaxy. I just attempted to connect our sequencer for the first time yesterday. I do not have an older version of galaxy to test and compare to see if it works in earlier versions. I am able to transfer data from the sequence to the import directory, however it is not moved to the data library. My data_transfer.log also has the same error. The server could not comply with the request since it is either malformed or otherwise incorrect. Does anyone have a solution for this? Thanks Emily -- Message: 17 Date: Wed, 28 Mar 2012 13:15:47 +0200 From: Leandro Hermida soft...@leandrohermida.com To: Luobin Yang yangl...@isu.edu Cc: Galaxy Dev galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever Message-ID: caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com Content-Type: text/plain; charset=ISO
Re: [galaxy-dev] How to add the option -c enabled to the qsub command?
Thanks for the link, Scott, I've confirmed that setting the job runner as pbs://machine.name/queue.name/-l nodes=n:ppn=m -c enabled/ in universe_wsgi does not work. Luobin On Mon, Nov 5, 2012 at 10:30 AM, Scott McManus scottmcma...@gatech.eduwrote: I recommend checking out John Chilton's dynamic job runner first: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html -Scott -- Hi, guys, I would like to enable checkpoint and restart for some galaxy jobs. In order to do that, I need to add -c enabled option when using qsub to submit a job. What files should I change to add this option? I am using Torque PBS job runner. Thanks, Luobin ___ 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/ ___ 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/
[galaxy-dev] Purge datasets without purging the associated history?
Hi, guys, Is it possible to purge some datasets in a history without purging the whole history? Thanks, Luobin ___ 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/
[galaxy-dev] Can I change the tool runner for set_metadata.sh?
Hi, guys, I noticed that set_metadata.sh is not in the tools folder as other tools. Can I set a tool runner for set_metadata.sh so that I can use specific resources (like specific compute node in the cluster) to run set_metadata.sh? Thanks, Luobin ___ 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/
Re: [galaxy-dev] Can I change the tool runner for set_metadata.sh?
Hi, Nate, Thanks for reply. Is it a standalone job that's dispatched when the edit attribute page is saved? Thanks, Luobin On Mon, Nov 12, 2012 at 12:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 12, 2012, at 12:38 PM, Luobin Yang wrote: Hi, guys, I noticed that set_metadata.sh is not in the tools folder as other tools. Can I set a tool runner for set_metadata.sh so that I can use specific resources (like specific compute node in the cluster) to run set_metadata.sh? Hi Luobin, Since set_metadata.sh must run after each tool, it is not run as a separate job, to avoid copying datasets multiple times for a single tool run. --nate Thanks, Luobin ___ 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/ ___ 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/
[galaxy-dev] Upgrade Python to a newer version.
Hi, Galaxy developers, My python version is 2.6.3 and I would like to upgrade it to 2.7.3. So is there anything that we need to on Galaxy after Python is upgraded to a new version? Thanks, Luobin ___ 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/
[galaxy-dev] galaxy.json?
Hi, When I run a job in my locally installed Galaxy, there is always an error message showing in the log file: Error opening galaxy.json file: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/005/5797/galaxy.json Any clue how to get rid of it? Thanks, Luobin ___ 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/
[galaxy-dev] lwr job runner error.
Hi, I checked out a refresh copy of latest galaxy-dist, but I found the following error in the log file after I ran Galaxy: galaxy.jobs.handler ERROR 2013-01-27 10:10:19,168 Job runner is not loadable: galaxy.jobs.runners.lwr Traceback (most recent call last): File /home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 447, in _load_plugin module = __import__( module_name ) File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 232 worker = threading.Thread( ( name=LwrJobRunner.thread-%d % i ), target=self.run_next ) ^ SyntaxError: invalid syntax Luobin ___ 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/
[galaxy-dev] sort the list of users while impersonating a user.
Hi, The list of users is not sorted when I try to impersonate a user, this is very inconvenient because of the large number of users in the system, is there a quick way to have users sorted ? Thanks, Luobin ___ 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/
[galaxy-dev] Different behavior of select tag in the tool configuration file when the number of options is different.
Hi, I have a 'select' tag in a tool's XML file, I would like to have a default option, which is choosing nothing. So the drop down menu of the web interface will be empty and when a user clicks the drop down menu, the list contains an empty entry with other options. So I basically have an option tag like the following option value=/option together with other options. This works fine when I have up to 19 options including the default options. A user can submit the job without selecting any options and the program will use the default option. However, when the number of options exceeds 20, then drop down menu of the web interface displays Click to Select or Search instead of empty. And the user has to select one of the options in order to submit the job, otherwise, a question mark is displayed in the drop down menu and then an error message shows up under the drop down menu with the message An invalid option was selected, please verify. Why the behavior changed when there are 20 options or more for a drop down menu? Thanks, Luobin ___ 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/
Re: [galaxy-dev] sort the list of users while impersonating a user.
I've got fix for this, add the following line between line 690 and line 691 in lib/galaxy/webapps/galaxy/controllers/admin.py : emails.sort() Thanks, Luobin On Tue, Jan 29, 2013 at 5:05 PM, Luobin Yang yangl...@isu.edu wrote: Hi, The list of users is not sorted when I try to impersonate a user, this is very inconvenient because of the large number of users in the system, is there a quick way to have users sorted ? Thanks, Luobin ___ 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/
[galaxy-dev] psiblast
Hi, Galaxy developers, I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed. Does it have one? Thanks, Luobin ___ 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/
Re: [galaxy-dev] psiblast
Hi, Peter, I mean the web interface for psiblast on Galaxy system, not the web interface at NCBI. Thanks, Luobin On Mon, Feb 4, 2013 at 10:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang yangl...@isu.edu wrote: Hi, Galaxy developers, I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed. Does it have one? Thanks, Luobin If you are asking about the ncbi_blast_plus suite in the Tool Shed, this has most of the key NCBI BLAST+ standalone tools now, but not yet psiblast or rpsblast. Peter P.S. When you said web-interface, did you mean to the NCBI online server? As far as I know there are no Galaxy interfaces to that - just for the standalone NCBI command line tools. ___ 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/
Re: [galaxy-dev] psiblast
Hi, Peter, What difficulties did you see to include psi-blast and phi-blast when you were working on the other programs in the NCBI+ suite? I would be interested in creating a tool configuration file for each of these two. Thanks, Luobin On Mon, Feb 4, 2013 at 10:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang yangl...@isu.edu wrote: Hi, Galaxy developers, I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed. Does it have one? Thanks, Luobin If you are asking about the ncbi_blast_plus suite in the Tool Shed, this has most of the key NCBI BLAST+ standalone tools now, but not yet psiblast or rpsblast. Peter P.S. When you said web-interface, did you mean to the NCBI online server? As far as I know there are no Galaxy interfaces to that - just for the standalone NCBI command line tools. ___ 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/
Re: [galaxy-dev] psiblast
Hi, Peter, Thanks for pointing them out! The phi-blast and psi-blast actually share the same binary, both use the psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is used, then it does phi-blast searching. Best, Luobin On Mon, Feb 4, 2013 at 11:14 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang yangl...@isu.edu wrote: Hi, Peter, What difficulties did you see to include psi-blast and phi-blast when you were working on the other programs in the NCBI+ suite? I would be interested in creating a tool configuration file for each of these two. Thanks, Luobin Hi Luobin, At first glance, the binaries for psiblast, rpsblast, and rpstblastn don't look too different for wrapping. We would need to define a third loc file for the RPS BLAST domain databases (like the existing loc files for nucleotide and protein databases). However, I'm not immediately sure where phi-blast existing with the standalone NCBI BLAST+ tools. Do you know? 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/
Re: [galaxy-dev] psiblast
Hi, Peter,
You are right, I thought there was already a datatype defined for PSSM, but
it turned out there isn't one yet. I attached a draft tool configuration
file for psiblast, it was based on the blastp configuration file, please
revise as you like.
The options that are specific to psiblast are the following:
1. num_iterations
2. pseudocount
3. inclusion_ethresh
Other options should be the same as the blastp program. So a typical
command line would be the same as blastp except adding above options if
non-default values are used. I can see there are two optional output files,
one is the PSSM and the other is ASCII PSSM. Besides using a typical query
input, psiblast can take a PSSM file or a multiple sequence alignment file
as the input.
Luobin
On Tue, Feb 5, 2013 at 4:53 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Mon, Feb 4, 2013 at 7:32 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Monday, February 4, 2013, Luobin Yang wrote:
Hi, Peter,
Thanks for pointing them out!
The phi-blast and psi-blast actually share the same binary, both use the
psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern
is
used, then it does phi-blast searching.
Best,
Luobin
Could you give a few command line examples of how you typically use
psiblast, focussing in the main options only?
I would find that helpful when putting together a new wrapper - since
including all the options right away is overwhelming.
Thanks,
Peter
I suspect we would also need to define another datatype for the PSSM
pattern files. That makes things more complicated.
Peter
tool id=ncbi_psiblast_wrapper name=NCBI BLAST+ psiblast version=0.0.15
descriptionSearch protein database with protein query sequence(s)/description
!-- If job splitting is enabled, break up the query file into parts --
parallelism method=multi split_inputs=query split_mode=to_size split_size=1000 shared_inputs=subject,histdb merge_outputs=output1/parallelism
version_commandpsiblast -version/version_command
command
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
psiblast
#if str($input_opts.input_opts_selector) == query
-query $query
#else if str($input_opts.input_opts_selector) == pssm
-in_pssm $in_pssm
#else if str($input_opts.input_opts_selector) == msa
-in_msa $in_msa
#end if
#if $db_opts.db_opts_selector == db:
-db ${db_opts.database.fields.path}
#elif $db_opts.db_opts_selector == histdb:
-db ${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}
#else:
-subject $db_opts.subject
#end if
-evalue $evalue_cutoff
-out $output1
##Set the extended list here so if/when we add things, saved workflows are not affected
#if str($out_format)==ext:
-outfmt 6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen
#else:
-outfmt $out_format
#end if
-num_threads 8
#if $adv_opts.adv_opts_selector==advanced:
$adv_opts.filter_query
-matrix $adv_opts.matrix
## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
## Note -max_target_seqs overrides -num_descriptions and -num_alignments
#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) 0):
-max_target_seqs $adv_opts.max_hits
#end if
#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) 0):
-word_size $adv_opts.word_size
#end if
##Ungapped disabled for now - see comments below
##$adv_opts.ungapped
$adv_opts.parse_deflines
## End of advanced options:
#end if
#if $psiblast_opts.psiblast_opts_selector==advanced
-num_iterations $psiblast_opts.num_iterations
-pseudocount $psiblast_opts.pseudocount
-inclusion_ethresh $psiblast_opts.inclusion_ethresh
#end if
#if $pssm_output_condition.pssm_output_selector == yes
-out_pssm $pssm_output
#end if
#if $pssm_ascii_output_condition.pssm_ascii_output_selector == yes
-out_ascii_pssm $pssm_ascii_output
#end if
/command
stdio
!-- Anything other than zero is an error --
exit_code range=1: /
exit_code range=:-1 /
!-- In case the return code has not been set propery check stderr too --
regex match=Error: /
regex match=EXception: /
/stdio
inputs
conditional name=input_opts
param name=input_opts_selector type=select label=Select the input file type
option value=query selected=trueQuery/option
option value=msaMultiple Sequence Alignment file/option
option value=pssmPSI-BLAST checkpoint file/option
/param
when value=query
param name=query type=data format=fasta label=Protein query sequence(s)/
/when
when value=msa
param name=in_msa type=data format=msa,phylip label=Multiple Sequence Alignment File /
/when
when value=pssm
param name=in_pssm type=data
[galaxy-dev] Divide the web interface into sections for a tool.
Hi, Galaxy developers, I would like to have the parameters on the web interface to be packed into sections for a tool. Is there a way to do this? There is a page tag, but the document says we should avoid using it. Also there is no replacement tag for page. The problem using the page tag is that there seems missing a previous step button on the pages other than the first page. If there is a section tag to be rendered as a box with a title and all the tags inside that section are rendered inside the box, that would be great. Even a horizontal bar to separate the sections is helpful. Thanks, Luobin ___ 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/
[galaxy-dev] What image formats can be displayed in the Galaxy view panel?
Hi, I tried the pcx and ps formats, but the browser just downloads these kinds of files instead rendering them in the Galaxy window... It seems png and pdf files can be rendered in the Galaxy windows. How can I make Galaxy display other image formats like ps and pcx? Thanks, Luobin ___ 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/
Re: [galaxy-dev] What image formats can be displayed in the Galaxy view panel?
Ross Peter, Thanks for clarifying on this! Luobin On Thu, Feb 7, 2013 at 4:36 PM, Ross ross.laza...@gmail.com wrote: Luobin - one additional minor observation: In reality, Galaxy does not do the displaying - it just sends stuff to the users' web browser for display. So even when Galaxy knows what mimetype to attach to a specific image file, the users' web browser response to that mimetype will always remain the final frontier. Not everyone uses IE where dark magic just happens :) Out of the box, many linux distributions do not enable (potentially exploitable) browser plugin viewers for PDF or SVG for example - so correctly displaying some mimetypes will always be beyond the control of the Galaxy server. EG: in 12.04 Ubuntu on my desktop using chrome or firefox, automagic pdf viewing on a 64 bit system took a fair bit of fiddling to get working - until then, even when Galaxy supplies the required mimetype, the user has to download the PDF and open it by hand. On Fri, Feb 8, 2013 at 10:16 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Feb 7, 2013 at 9:41 PM, Luobin Yang yangl...@isu.edu wrote: Hi, I tried the pcx and ps formats, but the browser just downloads these kinds of files instead rendering them in the Galaxy window... It seems png and pdf files can be rendered in the Galaxy windows. How can I make Galaxy display other image formats like ps and pcx? Thanks, Luobin I would guess this is possible but only if those other image types are first defined in Galaxy as new datatypes (with sensible MIME type values). 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/ -- +++ Luobin Yang, Ph.D. INBRE Bioinformatics Coordinator Research Assistant Professor Department of Biological Sciences, Idaho State University 921 S. 8th Ave., Stop 8007 Pocatello, ID 83209-8007 Office: 208-282-5841 ___ 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/
[galaxy-dev] Problem with get data/uploading file.
Hi, guys, Recently I found the Upload File tool under the Get Data category runs forever on my locally installed Galaxy system. It worked fine for a long time, but now it's not working anymore. Have you guys experienced similar things? Thanks, Luobin ___ 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] Empty or 'no peek' output.
This is strange: when I submit a job through the computers on campus to my locally installed Galaxy, the job finishes without no problem, but when I submit the same job through a computer off-campus, the job generates empty or 'no peek' output. What's causing the problem? Luobin ___ 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/
