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ToolShed test failure, "blastxml" ItemNotFoundError
by Peter Cock 23 Apr '13

23 Apr '13

Hi all, I'm seeing a unit test failure on the Tool Shed which I think is in some way related to the blast_datatypes dependency not refreshing the list of available file formats: http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr Revision: 7:a7add03a44fd - blastxml_to_top_descr v0.0.6 Tool shed version: 9471:ae53deed05b6 Galaxy version: 9505:1e3d92ec22b2 Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 43, in do_it shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 193, in upload_file self.refresh_form( "file_type", ftype ) #Refresh, to support composite files File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 1276, in refresh_form tc.fv( f.name, control.name, value ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 450, in formvalue set_form_control_value(control, value) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/utils.py", line 190, in set_form_control_value raise ClientForm.ItemNotFoundError('cannot find value/label "%s" in list control' % (val,)) ItemNotFoundError: cannot find value/label "blastxml" in list control This bug reminds me of something recently discussed on the list, but I can't find the thread (perhaps it was another file format). So there may already be a Trello issue open for this. Thanks, Peter

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Automatics Tool Shed tests - failed dependency installation?
by Peter Cock 22 Apr '13

22 Apr '13

Hi all, Over on the test Tool Shed, I'm trying to include automated installation of NLStradamus as part of my wrapper for this NLS prediction tool. This should make things simper for end users, but is also intended to get the unit tests to pass on the Galaxy Tool Shed setup. The repo is here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus The unit tests are still failing, just saying: Fatal error: Exit code 127 () /bin/sh: 1: NLStradamus: not found The tool XML file contains an explicit package dependency: <requirements> <requirement type="binary">NLStradamus</requirement> <requirement type="package" version="1.8">NLStradamus</requirement> </requirements> That package dependency is defined using the tool_dependencies.xml file (in the same repository). My tool_dependencies.xml file should compile this binary, and have it added to the $PATH. This error message suggests that this did not work: <?xml version="1.0"?> <tool_dependency> <package name="NLStradamus" version="1.8"> <install version="0.0.1"> <actions> <action type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8…</action>  <action type="shell_command">g++ NLStradamus.cpp -o NLStradamus -O3</action> <action type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> ... My question is was my tool_dependencies.xml file processed, and if so did it run without errors, and if so why didn't it work? If there were errors processing the tool_dependencies.xml then I would hope the ToolShed would show them (and not silently overlook this and attempt to run the tests anyway). Is that the case? Thanks, Peter

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Problem uploading file !!
by Nishant THAKUR 22 Apr '13

22 Apr '13

Hello, I installed galaxy server on ubuntu recently, I can upload small fastq files (~600 Mb), but when I am uploading large file(2.7 gb), it is taking forever. Could you please suggest me something ? Best regards Nishant Thakur

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download URLs limited to twelve?
by Shantanu Pavgi (Campus) 21 Apr '13

21 Apr '13

One of our users is trying to download thousands of files by pasting their URLs in 'URL/Text' box of the upload tool. It seems like Galaxy selects only first 12 URLs and ignores rest of them. The issue can be reproduced on the main public Galaxy<https://main.g2.bx.psu.edu/> instance as well. I was wondering how can we remove this limit so that users can queue up thousands of download jobs in one click. Any help? -- Thanks, Shantanu

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directory copies as zero-length file from job_working_directory?
by Nikhil Joshi 20 Apr '13

20 Apr '13

Hi all, So I have a tool that I am writing a wrapper script for that produces a directory of images as one of its outputs. This directory gets created just fine in the job_working_directory, but then when the job finishes and the contents of the job_working_directory are copied, the copy of the images directory is a zero-length *file*. I seem to recall having this problem before and finding a solution to it, but now I can't seem to find it. Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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Knowing who is currently logged into your system
by Jennifer Jackson 20 Apr '13

20 Apr '13

Hi Akshay, I am going to post your question over to the galaxy-dev(a)bx.psu.edu mailing list, to give it better viability. You could probably run an sql query against a database table to find out this information, but there may be a better way. Let's see if someone has a method worked out they want to share. Another alternative is to look in our documentation, ReadTheDocs. I did a search on "login" and a few potentials popped up: http://galaxy-dist.readthedocs.org/en/latest/ Going forward, the galaxy-dev list is the list you will want to post to - and consider subscribing to - if you are running a local instance and want to join/discuss issues with the community of other users doing the same. http://wiki.galaxyproject.org/MailingLists http://wiki.galaxyproject.org/Support#Mailing_Lists Thanks! Jen Galaxy team On 3/12/13 5:46 PM, Akshay Vivek Choche wrote: > Hello All, > > I was wondering if there is a way to know all the users logged into your local galaxy server? > > Thanks, > -Akshay Choche > > ___________________________________________________________ > 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Error in universe_wsgi.ini regarding gzip
by Perez, Ricardo 19 Apr '13

19 Apr '13

Dear all, I have encountered a problem where my browser does not show the history sidebar in galaxy. In my configuration I had the following line in universe_wsgi.ini uncommented, which seem to be the source of the problem. #filter-with = gzip Commenting that line will fix my browser and see the history bar again. Thanks, --Ricardo Perez

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Errors when starting galaxy
by Perez, Ricardo 19 Apr '13

19 Apr '13

Dear all, I get the following errors when starting galaxy, is there any way to fix this. Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py", line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in parse_xml tree = ElementTree.parse(fname) File "/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py", line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, in parse_xml tree = ElementTree.parse(fname) File "/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") Best, --Ricardo Perez

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ToolShed functional tests bug
by Peter Cock 19 Apr '13

19 Apr '13

Hi all, I've been looking at the new functional test results now being shown on the tool shed, and found a bug/glitch: 1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 2. Click on top right menu "Repository Actions", "View functional test results" menu item 3. Notice two failed tests for htseq_count (which is not in this repo) This was for 12:6753a9261390 of this repo. Peter

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TestToolShed out of date? (not running unit tests)
by Peter Cock 19 Apr '13

19 Apr '13

Hi all, I'd like to be able to experiment with the new automated testing recently added to the main Tool Shed http://toolshed.g2.bx.psu.edu/ by first trying my updates on the Test Tool Shed (to make sure my tests will work before making the tool update public). It appears that the testing features are not available on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/ Is this correct? Is this intentional? Thanks, Peter P.S. This would be less urgent if I could solve this issue which is blocking my local testing: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014123.html

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