April 2014 - galaxy-dev - lists.galaxyproject.org

the dataset update time
by Sanka, Ravi 24 Apr '14

24 Apr '14

Greetings, Just have a conceptual question regarding the dataset object's field update time. What events trigger this field to get modified? For example, I know that using admin_cleanup_datasets.py will update the dataset's update time if it matches the given parameters. What other triggers are there? Are there any actions via UI that will update the update time, such as downloading or even just viewing the dataset's contents? ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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cleaning up job_working_directory
by Sanka, Ravi 24 Apr '14

24 Apr '14

Greetings, Currently my group has set our universe_wsgi.ini's cleanup_job to "onsuccess", allowing us to troubleshoot failed runs. However, now failed job folders are beginning to accumulate in the job_working_directory. Is there a way to clean this up? Preferably, a means that can be automated, like with the cleanup_datasets scripts. ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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errors with startup of galaxy server
by Tony Kusalik 24 Apr '14

24 Apr '14

Hi, On April 16th, I did an hg incoming command to update my local version of Galaxy. Once I restarted my server, I was told to do sh ./scripts/migrate_tools/0010_tools.sh take care of tools which had been migrated to the tool shed. Ever since the two changes above, I am seeing strange errors in paster.log that I do not understand. Here are some samples: (Note that Galaxy is installed in directory /birl2/Galaxy.) -- begin paste -- galaxy.tools ERROR 2014-04-23 12:29:48,869 Error reading tool from path: data_source/bx_browser.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' galaxy.tools ERROR 2014-04-23 12:29:48,921 Error reading tool from path: data_source/flymine_test.xml Traceback (most recent call last): File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 544, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 658, in load_tool tree = load_tool( config_file ) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/birl2/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 154, in parse_xml tree = ElementTree.parse(fname) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") -- end paste -- This pattern of error messages continues for/from flymine_test.xml, mousemine.xml, ratmine.xml, yeastmine.xml, metabolicmine.xml, encode_db.xml, epigraph_import.xml, epigraph_import_test.xml, epigraph.xml, epigraph_test.xml, gencode_partition.xml, random_intervals.xml, column_join.xml, wiggle_to_simple, phastOdds_tool.xml. The general theme is the constant reference to "elementtree-1.2.6_20050316-py2.7.egg". Also of note is that an ls command says that /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg is a regular file, and not a directory. Within the Galaxy Admin window, I tried to search for tools (either installed or available) matching "ElementTree" but couldn't find anything. Further, checking paster.log files from prior to having given the sh ./scripts/migrate_tools/0009_tools.sh command, I see /birl2/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg mentioned in the python path given at the beginning of paster.log, but no error messages involving "ElementTree" or "elementtree". How do I deal with this problem, and get the server to come up error free? Any suggestions would be welcome.

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Re: [galaxy-dev] Help Galaxy
by Enis Afgan 24 Apr '14

24 Apr '14

Hello, Galaxy workflow and history structure is stored in Galaxy's database vs. flat files so you can't just find the representation of those on the file system. I actually don't know if there is any documentation about the JSON structure for those artifacts - I've CC'd the -dev mailing list so someone there might know (btw, emailing the -dev list is preferred with questions like these because your question get more exposure). In the mean time, you can explore the API documentation (available here<http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-b…>and here<https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.…>) because that's where JSON objects can be retrieved. Hope this helps, Enis On Thu, Apr 24, 2014 at 3:33 PM, yattara Moussa <moussayattara2(a)yahoo.fr>wrote: > Hello, > I'm working at South Paris University (Université Paris-Sud) Computer > Science Research Laboratory (LRI), France. > > I'm working on Galaxy. > > I need to know about Galaxy syntax for worklfow internal structure > description with JSON, and Galaxy workflow history. > > *if you have any technical document describing the JSON syntax used for > the storage of Galaxy workflow and Galaxy history, it will be very nice if > you can send it to me. > > *I installed Galaxy on ubuntu, In which directory can I find workflow > histories files ?. > > Thank you for your considération, I look forward to hearing from you. > > Moussa YATTARA. > >

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(New) error in Galaxy Reports
by Nikos Sidiropoulos 24 Apr '14

24 Apr '14

Hi all, a similar error with this one ( http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html) has appeared in Galaxy reports after the last update. It also occurs only when I'm trying to view the completed jobs in a certain day. Thanks in advance. Bests, Nikos

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Specifying _JAVA_OPTIONS in job_conf.xml
by Björn Grüning 24 Apr '14

24 Apr '14

Hi, to specify -Xmx and -Xms for java based programs I set my preferred values to $_JAVA_OPTIONS and include _JAVA_OPTIONS as nativeSpecification with -v _JAVA_OPTIONS. That worked good so far, but the downside is that I can not have different options for different tools. Is there a trick I can specify arbitrary $ENVs to a specific tool? Any ideas how to solve that, without hacking the -Xmx and -Xms parameters into the wrapper file? It is related to https://trello.com/c/HGEYPQf6. I would be interested in workarounds until that card is closed :) Something like that would be great: <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner" destination="10G_memory"> <param id="nativeParam">export _JAVA_OPTIONS='-Xmx=6GB'</param> </tool> Thanks! Bjoern

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy Biostar) you will be automatically logged in. * A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account’s password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get started at https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at http://biostar.usegalaxy.org and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transition but starting now please use the biostar.usegalaxy.org forum to ask all questions about using Galaxy. * Please do not double post to both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post "Welcome to Biostar" to tell us what you think. What’s next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! The Galaxy team

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

* Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org <https://biostar.usegalaxy.org/>! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on *usegalaxy.org <http://usegalaxy.org>*, a***<https://usegalaxy.org/cloud>**Cloudman <http://usegalaxy.org/cloud> *instance, or any other <https://wiki.galaxyproject.org/PublicGalaxyServers> *Galaxy <http://getgalaxy.org>*, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from *usegalaxy.org* <http://usegalaxy.org> (Top*m*enu: "Help ->Galaxy Biostar")you will be automatically logged in. A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account's password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get startedat https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at *http://biostar.usegalaxy.org*and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transitionbut starting now please use the biostar.usegalaxy.org <http://biostar.usegalaxy.org>forumto ask all questions about using Galaxy. * Please do not double postto both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post *"Welcome to Biostar"* to tell us what you think. What's next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! *Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>* *

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FTP page not viewable.
by Timothy Carr 23 Apr '14

23 Apr '14

Hi All, I've discovered a strange FTP related issue with Galaxy. All was working well until recently when I attempted to view files which I uploaded via FTP. The FTP page view was not being displayed and does not display the files in the Galaxy interface. No updates were applied. I've restarted Galaxy but unfortunately does not resolve the issue. Is there some of sort page cache in galaxy which needs to be cleared ? Any suggestions would be appreciated. Regards Tim

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problem with bioc_qvalue, Version: 1.34.0
by Tony Kusalik 22 Apr '14

22 Apr '14

Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with "bioc_qvalue" or "11735242a19e" but nothing was turned up. Tony Kusalik

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