galaxy-dev March 2014

galaxy-dev@lists.galaxyproject.org

101 participants
141 discussions

Galaxy startup takes very long. Normal?
by Geert Vandeweyer 27 Mar '14

27 Mar '14

Dear all, I'm wondering if the following behaviour is normal. Since I reinstalled the latest galaxy distribution, every restart hangs/loads for up to 10 minutes at the following lines: galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 118 tool_shed.galaxy_install.migrate.check INFO 2014-03-25 15:56:58,477 At migrate_tools version 9 galaxy.config INFO 2014-03-25 15:56:58,694 Install database targetting Galaxy's database configuration. After several minutes of no heavy processing (cpu/database is almost idle), the startup continues. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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Errors loading data into IGV from Galaxy
by Hillman, Paul R. 26 Mar '14

26 Mar '14

Dear Galaxy Team, I have already contacted IgV about this issue and they say that I needed to contact you. I have had and instance of IgV shared with me for some time and it has worked as recently as last week. However, even last week the data was only loading approximately 25% of the time and now will not load at all. Could you please explain the error that I am getting below and what can be done to correct them. Unfortunately the individual who created and shared these files is no longer in the lab so I do not have direct access to the data. Any help would be greatly appreciated. Sincerely, -Paul Hillman- Errors were encountered loading the session: https://main.g2.bx.psu.edu/display_application/b35f82886ba2954e/igv_bam/web… &nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) https://main.g2.bx.psu.edu/display_application/70deaaa1fc17635d/igv_bam/web… &nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500)

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YAML Configuration, select specific file
by Dooley, Shane 26 Mar '14

26 Mar '14

Is anyone aware of how to specify a field in the nglims.yaml that will allow me to select a specific dataset from my current history (or even a chosen history)? I know that I can use type: HistoryField to select a history but how do I specify a type that allows me to choose a dataset from a history or from my current history? Thanks, Shane This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. The dupont.com<http://dupont.com/> web address will continue in use for a transitional period for communications sent or received on behalf of DuPont Performance Coatings., which is not affiliated in any way with the DuPont Company. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html

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Recovery of lost DRMAA job?
by Brian Claywell 25 Mar '14

25 Mar '14

We're having a slight issue with some of the jobs our Galaxy instance is submitting to the cluster via the DRMAA runner. Our cluster admin thinks it's not Galaxy's fault, but the problem results in some odd behavior in Galaxy, as follows. From galaxy.log: galaxy.jobs.runners.drmaa INFO 2014-03-25 12:17:46,950 (1667/5806401) job left DRM queue with following message: code 1: slurm_load_jobs error: Socket timed out on send/recv operation,job_id: 5806401 galaxy.jobs.runners ERROR 2014-03-25 12:17:50,272 (1667/5806401) Job output not returned from cluster: [Errno 2] No such file or directory: '/galaxy/database/job_working_directory/001/ 1667/galaxy_1667.o' galaxy.jobs.output_checker INFO 2014-03-25 12:17:50,379 Job 1667: Log: tool progress galaxy.jobs.output_checker INFO 2014-03-25 12:17:50,379 Job 1667: Log: tool progress galaxy.jobs DEBUG 2014-03-25 12:17:51,123 job 1667 ended 1. As best we can tell, for some reason the socket Galaxy's using to keep track of the job times out (this is the part we don't think is Galaxy's fault). The job continues to run on the cluster, but: 2. When the socket times out, Galaxy checks to see if the redirected stdout file exists, but since the job's still running, it doesn't exist, and so it throws an error... 3. ... and eventually Galaxy just gives up on the job entirely. This seems strange, considering Galaxy so gracefully recovers jobs when it's restarted; I admit I'm not familiar with the mechanics of tracking a job, but would a few retries spaced out over a few minutes be appropriate here, if that's possible? Failing that, is there a way to manually recover it, or could such a way be added? This job will probably run for days, and it would be nice not to have to manually collect the outputs and send them back to the user! What ends up happening in the Galaxy interface is that the history items turn green as if they completed successfully, but of course they're completely empty, which was a bit of a confusing thing for the user that was having this problem. Thanks! -- Brian Claywell, Systems Analyst/Programmer Fred Hutchinson Cancer Research Center bclaywel(a)fhcrc.org

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Dealing with qiime output
by Ravi Alla 25 Mar '14

25 Mar '14

Hello galaxy devs, I installed qiime-galaxy to my local galaxy (running jobs on a cluster). The split_libraries.py tool outputs a dir of files. How do I go about displaying these files in the history panel after the tool finishes running? I have been trying to look at the composite datatypes guide, but I really am having a hard time wrapping my head around it. Should I be creating a new composite datatype for any tool that outputs directories (each with diff files to display). Is there anyway to have galaxy automatically unzip output directories to history? Thanks Ravi

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 25 Mar '14

25 Mar '14

Hello all, *We are pleased to announce that Early Registration <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and Poster Abstract Submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for the 2014 Galaxy Community Conference (GCC2014) <https://wiki.galaxyproject.org/Events/GCC2014>.* GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *Early registration <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. *Abstract submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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create local galaxy in mac os
by Chunjiang He 25 Mar '14

25 Mar '14

I am adding tools to local galaxy and encountered some problems. when I install samtools from Tool Shed, it stays on "installing dependent tools" for long time. I am not sure where is the problem. Anyone can help. Or I would like to create XML myself for downloaded packages. How to do that? Thanks, Cam

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Re: [galaxy-dev] I can't impersonate an user
by Eric Kuyt 25 Mar '14

25 Mar '14

Hi Dannon, could this still be existent in galaxy-dist? Impersonate.mako<https://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c1096…> doesn't seem to have "${h.url_for(controller="/api/users", action="index")}" in its source and tries to find /api/user on the server root. Thanks, Eric On 17 March 2014 16:31, Dannon Baker <dannon.baker(a)gmail.com> wrote: > 694411e94d9a

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Re: [galaxy-dev] prims workflows
by Greg Von Kuster 25 Mar '14

25 Mar '14

Hello Pieter, When you install a repository into Galaxy that contains workflows, you can import the workflow into Galaxy. At the time the workflow is imported, the import process checks to see if all required tools are available in Galaxy. If not, a page is displayed with links to accessible Tool Sheds allowing the user to search for missing required tools. I believe this still works, although there have been some changes to the workflow framework over the past several months, and I have not checked to see if this is still available. See https://wiki.galaxyproject.org/ToolShedWorkflowSharing for more details. This approach is basically a "hack" that I implemented several years ago. A much better approach would be to enhance the workflow UI to include a feature allowing the user to search Tool Sheds to discover and install missing tools required by any workflow currently abvailable in the Galaxy instance. Hopefully at some point soon something like this will be introduced. Greg Von Kuster On Mar 25, 2014, at 6:47 AM, "Lukasse, Pieter" <pieter.lukasse(a)wur.nl> wrote: > Hi Bjoern, > > I think you may have misunderstood me. What I mean is : instead of me having to add a tool_dependencies or repository_dependencies.xml to the workflows package, let Galaxy Tool Shed find these dependencies based on metadata available in the workflow itself. > > Best regards, > > Pieter. > > -----Original Message----- > From: Björn Grüning [mailto:bjoern.gruening@gmail.com] > Sent: dinsdag 25 maart 2014 11:43 > To: Lukasse, Pieter; Greg Von Kuster (greg(a)bx.psu.edu) > Subject: Re: FW: prims workflows > > Hi Pieter, > > if I'm not misunderstood you, thats already possible: > > Have a look at: > https://github.com/bgruening/galaxytools/tree/master/workflows/glimmer3 > > For an example. > Cheers, > Bjoern > > Am 25.03.2014 11:08, schrieb Lukasse, Pieter: >> Hi Greg, >> >> Do you have any plans of resolving the dependencies automatically when it comes to workflows? E.g. I have a Tool Shed repository where I would like to add workflows that are constructed using tools from different repositories. It would be nice if you could let Tool Shed install the tools automatically upon installation of the workflow. Any plans? >> >> Best regards, >> >> Pieter >> >> -----Original Message----- >> From: Björn Grüning [mailto:bjoern.gruening@gmail.com] >> Sent: zaterdag 22 maart 2014 16:25 >> To: Lukasse, Pieter >> Subject: prims workflows >> >> Hi Pieter, >> >> thanks for your prims Galaxy contributions. >> Any chance to add a repository_dependencies.xml file to the workflow repository? >> >> Thanks, >> Bjoern >> >> > > >

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tool_dependencies.xml Environmental Variable Question
by Michael E. Cotterell 25 Mar '14

25 Mar '14

Is the expected behavior that environmental variables setup in a tool’s tool_dependencies.xml file are not available in the tool’s python virtualenv during runtime? It’s seems odd that we can specify modules (installable from pip) that are available during runtime, but that the environmental variables are not available during runtime. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/

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galaxy-dev March 2014