galaxy-dev July 2011

galaxy-dev@lists.galaxyproject.org

79 participants
166 discussions

Getting a list of workflows a user can run via the API
by Duddy, John 26 Jul '11

26 Jul '11

I am doing an integration with Galaxy, and part of what I need to do is trigger workflows. To do that, I need to list them. I can do this if the user owns the workflows, but the API does not return workflows that have been shared with the user. Is there a way via the API to discover the sharing relationships? Or will I need to add this to the API? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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set_matadata_externally =True
by Chorny, Ilya 26 Jul '11

26 Jul '11

I am still working on the patch to submit jobs as the actual user under SGE . I have it working for the default case but it fails for the case of set_metadata_externally = TRUE. Can someone point me to where the metadata files are created so that I can change the permissions for those files? Also, I have to addusers to the galaxy group in order for this to work because the galaxy_*.sh scripts are created as executable only by members of the galaxy group. I want to change this so that all users can execute these scripts. Any help on where in the code these scripts are created? Upon completion I will create a galaxy central fork and upload my changes to it. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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API workflow_execute.py using ldda
by Andrew Warren 26 Jul '11

26 Jul '11

Hello, I have been working on running a workflow programmatically on my local galaxy instance using library datasets. It took me a few hours to figure out the problem I was having so I thought I would document it here in case it helps anyone. Also, I have a question regarding 'ldda' IDs (see below). After looking at this post: http://gmod.827538.n3.nabble.com/Running-a-workflow-programatically-td25725… the comments in workflow_execute.py I was trying to run a workflow in the following way: 1) get the dataset ID's from the library ./display.py <api_key> http://localhost:8080/api/libraries/ebfb8f50c6abde6d/contents Collection Members ------------------ #1: /api/libraries/ebfb8f50c6abde6d/contents/c6ca0ddb55be603a016bf252082cbf1f name: / type: folder id: c6ca0ddb55be603a016bf252082cbf1f #2: /api/libraries/ebfb8f50c6abde6d/contents/a0e1686ccf7a028a name: /http://smane.vbi.vt.edu/SRR014335.fastq type: file id: a0e1686ccf7a028a #3: /api/libraries/ebfb8f50c6abde6d/contents/98a64dc1a6526c8e name: /http://smane.vbi.vt.edu/SRR014339.fastq type: file id: 98a64dc1a6526c8e #4: /api/libraries/ebfb8f50c6abde6d/contents/2764e29c8c7b7454 name: /http://smane.vbi.vt.edu/Yeast.gtf type: file id: 2764e29c8c7b7454 2) get input IDs for the workflow ./display.py <api_key> http://localhost:8080/api/workflows/f2db41e1fa331b3e Member Information ------------------ url: /api/workflows/f2db41e1fa331b3e inputs: {'102': {'value': '', 'label': 'Illumina2'}, '104': {'value': '', 'label': 'ReferenceAnnotation'}, '96': {'value': '', 'label': 'Illumina1'}} id: f2db41e1fa331b3e Then I ran: python /opt/galaxy_server/galaxy-dist/scripts/api/workflow_execute.py <api_key> http://localhost:8080/api/workflows f2db41e1fa331b3e 'Test API' '102=ldda=a0e1686ccf7a028a' '104=ldda=2764e29c8c7b7454' '96=ldda=98a64dc1a6526c8e' This gives the following error at the end of the stack trace for HTTP Error 500: *ValueError: invalid literal for int() with base 10: 'file.37'* * * After looking through the code for a while I saw that when the "src id type" is given as "ld" then the decoded name is split and the number is used to retrieve the ldda or "library_dataset_dataset_association" So instead I ran the above command with: '102=ld=a0e1686ccf7a028a' '104=ld=2764e29c8c7b7454' '96=ld=98a64dc1a6526c8e' And everything worked, woo! This brings me to my question: Where can I find ldda ID's ? I imagine I could find them in my database and there looks like some functions in lib/galaxy/web/api/workflows.py for handling them but I am having trouble locating them via an API script or on the library management interface. Note: I am assuming that the ID's returned by display.py are in fact "ld" ID's since this is the ID type I used to avoid the error listed above. Thanks, Andrew

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Question about dependency management
by Singh, Indresh 25 Jul '11

25 Jul '11

Greetings, We installed Galaxy at JCVI for internal user but we are discovering that we are missing lots of third party tools/dependencies. My question; is there any script/tool that we can use to checks for all Galaxy dependency software. Also is there any test suite that you guys use to make sure there are no major issues before release. If yes then we can use that test suite to verify our local install and identify any missing dependencies. Thanks again in advance. Regards, Indresh Singh J. Craig Venter Institute(JCVI) 9704 Medical Center Drive Rockville, MD 20850, USA Phone: (301)-795-7129 Fax: (240)-243-0600 www.jcvi.org<http://www.jcvi.org>

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Re: [galaxy-dev] Saved Histories - default view on deleted histories (bug)
by Jeremy Goecks 25 Jul '11

25 Jul '11

Jack, Thanks for following up on this issue. I've fixed the problem in galaxy-central changeset c176363cb7b2: https://bitbucket.org/galaxy/galaxy-central/changeset/c176363cb7b2/ Finally, please send all emails to our mailing lists rather than individual Galaxy developers or other list members. Sending email to the mailing lists ensures that everyone can see and contribute to questions and issues; in addition, emails to mailing lists are tracked and archived so that they are available in the future. Best, J. On Jul 18, 2011, at 11:25 AM, Yuelin Zhu wrote: > Hi Jeremy, > > Sorry for bugging you. But I have been trying to fix the history > problem with my local instance of Galaxy for a while. Basically all > the histories in my Galaxy go to deleted container, including previous > or new created ones (please see some screen shots in the attachments). > I even I tried a new instance of the galaxy-central and see the same > problem. The problem started two or three weeks ago after an update. > I noticed you fixed a similar (same?) bug > (https://bitbucket.org/galaxy/galaxy-central/issue/596/saved-histories-defau…), > so I bring my problem to your attention. Your help will be greatly > appreciated. Please let me know if you need any more information. > > Jack > ---- > Yuelin Jack Zhu

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Error preparing job
by SHAUN WEBB 25 Jul '11

25 Jul '11

Hi all, I'm getting the following error running a custom tool. I'm not really sure where the problem is coming from, it doesn't happen every time I run the tool. Can anyone point me in the right direction? Thanks Shaun Traceback (most recent call last): File "/storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.prepare() File "/storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/__init__.py", line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/storage/home/galaxy/test/galaxy-dist/lib/galaxy/tools/__init__.py", line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/storage/home/galaxy/test/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/storage/home/galaxy/test/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1311417753_92_55587.py", line 88, in respond NotFound: cannot find 'checktype' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Galaxy cloud installation in iPlant Atmosphere?
by Julin Maloof 23 Jul '11

23 Jul '11

Hi All (cross-posting to galaxy-dev and iplant support) The iPlant collaborative is running a "cloud" computer service based on the Amazon platform. https://pods.iplantcollaborative.org/wiki/display/atmosphere/iPlant+Atmosph… http://www.iplantcollaborative.org/discover/atmosphere I am interested in trying to get the cloud version of Galaxy running on an iPlant virtual machine. I was wondering if anyone had already done this? Thanks, Julin Julin Maloof Associate Professor Department of Plant Biology 1 Shields Ave University of California, Davis Davis, CA 95616 (530) 752 8077

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possible to undelete a history?
by Edward Kirton 23 Jul '11

23 Jul '11

An unfortunate user emailed me and said he accidentally deleted his histories. :(( How can I help him recover these?

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Apache Configuration for Exporting Histories and Workflows
by John Chilton 22 Jul '11

22 Jul '11

Hello All, We have Galaxy behind an apache proxy, and apache is taking care of the authentication. If I want to enable exporting workflows and histories to other galaxy instances do I just need to disable the authentication checks for locations "/history/export_archive" and "/workflow/for_direct_import"? I assume this wouldn't also open a hole that would allow unpublished workflows or histories to be accessed by others (at my institution or else wise), is this correct? Thanks for your time, -John ------------------------------------------------ John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton(a)msi.umn.edu

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Re: [galaxy-dev] Newer Version of Cufflinks Wrapper
by Jeremy Goecks 22 Jul '11

22 Jul '11

Ilya, A patch is fine for a one-time fix; this is easy with Mercurial: % hg diff > my_patch.patch However, if you plan to contribute to Galaxy on a regular basis, we encourage you to fork Galaxy and maintain your own Bitbucket repository. Finally, please send all emails to our mailing lists rather than individual Galaxy developers or other list members. Sending email to the mailing lists ensures that everyone can see and contribute to questions and issues; in addition, emails to mailing lists are tracked and archived so that they are available in the future. Thanks, J. On Jul 21, 2011, at 5:16 PM, Chorny, Ilya wrote: > I would be happy to share any changes that I make. By patch do you mean a diff/patch share patch or just check in the code? > > From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] > Sent: Wednesday, July 20, 2011 4:55 PM > To: Chorny, Ilya > Cc: galaxy-user-bounces(a)lists.bx.psu.edu; galaxy-dev(a)lists.bx.psu.edu > Subject: Re: [galaxy-dev] Newer Version of Cufflinks Wrapper > > Ilya, > > Despite the wrapper version numbers (which I'll update shortly to avoid further confusion), the current Cufflinks wrapper in both galaxy-central and galaxy-dist supports Cufflinks v1.0.3 However, not all new options for v1.0.3 are implemented the current wrappers; should you decide to implement additional options in the Cufflinks/compare/diff wrappers, please consider submitting a patch that we could incorporate into Galaxy. > > Best, > J. > > On Jul 21, 2011, at 1:30 AM, Chorny, Ilya wrote: > > > Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. > > Thanks, > > Ilya > > > > Ilya Chorny Ph.D. > Bioinformatics – Intern > ichorny(a)illumina.com > 858-202-4582 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >

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galaxy-dev July 2011