January 2015 - galaxy-dev - lists.galaxyproject.org

January 13, 2015 Galaxy Distribution
by Jennifer Hillman-Jackson 13 Jan '15

13 Jan '15

*January 13, 2015 Galaxy Distribution* <https://wiki.galaxyproject.org/News/2014_01_13_Galaxy_Distribution> [image: width=175] <http://getgalaxy.org/> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13>* Security Several *critical* security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This stable Galaxy release contains fixes for those vulnerabilities <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Security>. *The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.* IPython Integration Thanks to the awesome work of community members Björn Grüning and Eric Rasche, Galaxy now features integration with the popular IPython project <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#IPython_Integration>. The Galaxy-IPython <https://github.com/bgruening/galaxy-ipython> project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. Tool Form Upgrade (for Beta Testing) In Galaxy's development branch, the basic tool from has been redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Tool_Form_Upgrade_.…>. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default. Get The Distribution [image: getgalaxy] <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/GetGalaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2015.01.13 *Thanks for using Galaxy!* The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson http://galaxyproject.org

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Re: [galaxy-dev] Tool Development DELLY
by Peter Cock 12 Jan '15

12 Jan '15

Hi Marco, No problem - I originally copied the metadata access trick from one of the Galaxy dev-team's tool anyway. Maybe we need to add this to the wiki... Peter On Tuesday, January 13, 2015, Marco Albuquerque < marcoalbuquerque.sfu(a)gmail.com> wrote: > Hi Peter, > > I was unaware of how to access metadata, that seemed to be my issue. The > tool works now though! > > Thanks so much, > > Marco > > > > > On 2015-01-09 7:13 PM, "Peter Cock" <p.j.a.cock(a)googlemail.com > <javascript:;>> wrote: > > > >I think the symlink approach is best, see for example the Python > >wrapper script I used here for "samtools idxstats", > > > https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats > > > >However, you can make the link in the XML directly, see Dave's > >reworking of this wrapper: > > > https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection > >s/samtools/samtools_idxstats > > > >Regards, > > > >Peter > > >

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Re: [galaxy-dev] No API way to delete a galaxy data library folder?
by Dooley, Damion 12 Jan '15

12 Jan '15

Hi Martin - Following up on this - I think your API folder delete commit is : https://bitbucket.org/galaxy/galaxy-central/commits/8f76a6abc5d7d5c98b6c148… ? I was wondering how to find out more about this API call. Not knowing the guts of the Galaxy API code much, is it a call like: http://[my galaxy]/api/folders/[my folder id]/delete I haven't tested since I haven't played with "Next-stable" galaxy branch. When roughly does that get woven into stable or default? Regards, Damion > Martin Čech | Threaded | More > Dec 04, 2014; 4:40pm Re: No API way to delete a galaxy data library folder? > I have actually implemented this feature and it will be in the next release (which should be made public around next monday).

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Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library? (Nicola Soranzo)
by Dooley, Damion 12 Jan '15

12 Jan '15

> Hi Damion, > I finally got to implement this, see method copy_from_dataset() in this commit: > https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aa… Thanks Nicola! Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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Tool Development DELLY
by Marco Albuquerque 09 Jan '15

09 Jan '15

Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy. There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index. I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how. Any help is greatly appreciated, Marco

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Galaxy Bioblend option for importing dataset into a library?
by Dooley, Damion 09 Jan '15

09 Jan '15

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

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How to test my functional tests?
by Jeltje van Baren 08 Jan '15

08 Jan '15

Hi, I'm trying to find out what the best way is to see if my functional tests work as expected, and I'm also wondering when these tests are (supposed to be) run. Here are the details: Following instructions at https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial, I created a little toolExample tool under galaxy-dist/tools/myTools. I also created test input and output in a test-data directory and added a test to the toolExample.xml file: <tests> <test> <param name="input" value="testinput.fa"/> <output name="out_file1" file="testoutput.txt"/> </test> </tests> And yes, the files are named correctly: tools/myTools/test-data/testinput.fa tools/myTools/test-data/testoutput.txt I added the new tool to config/tools_conf.xml AND to config/tools_conf.xml.sample. Question #1: Why is a .sample file used by run_functional_tests.sh? I thought with .sample extensions were meant as examples for creating your own versions, I'm really surprised that any script would want to access these. I restarted galaxy to verify that the new tool showed up, then checked that I could test it: ./run_functional_tests.sh -list | grep fa_gc_content_1 It shows up in the list of tools. So then I tested it: ./run_functional_tests.sh -id fa_gc_content_1 This gives IOError: [Errno 2] No such file or directory: '/inside/home/jeltje/exp/varscan2/programs/galaxy-dist/test-data/testinput.fa' So it looks like at some point the testinput should have been copied to galaxy-dist/test-data but wasn't. Question # 2: Is there some setting that makes this test input (and output) get copied to the correct location, or do I have to do this manually? I also tried testing by uploading the tool to the testtoolshed (as jtest1). I deliberatly put the wrong value in the testoutput.txt file because I'd like to see a test fail before I'll accept that it succeeds. It appears the testinput does not get tested on upload, because I got no automated test results, and no error messages anywhere. Is that expected behavior? I know the tools get tested every so often, I'm just surprised it doesn't happen on upload. The tool could then also be easily installed to my galaxy distribution, without errors in my log or on the browser pages. Question #3: At what point in creating or downloading a repository are these tests run? And lastly, #4: is either of these the best way to test my tests, or did I overlook something? Thank you! -Jeltje

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Mercurial is out of date for Toolshed
by Ryan G 08 Jan '15

08 Jan '15

I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version?

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cluster queue job id?
by Anna Terry 08 Jan '15

08 Jan '15

Hi, Sorry if this is a stupid question, but is the job id and other queue info, for a job that has run on a cluster available from within galaxy? Both during and and after completion of the job. Many thanks Anna

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Text file busy
by Evan Bollig PhD 08 Jan '15

08 Jan '15

I get this error occasionally: "/bin/sh: 1: /opt/galaxy/web/database/job_working_directory/000/100/galaxy_100.sh: Text file busy" When this occurs, the step fails outright. Resubmitting the step resolves the issue and things run no problem. If this error appears early in a long workflow, I have to manually resubmit ALL dependent steps... what a pain! Perhaps this is something the Galaxy job scheduler can look out for, flush() the system, sleep() a second or two to let the file write and close, and then rerun. A more fault-tolerant way of running workflows without unnecessary human intervention. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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