- galaxy-dev - lists.galaxyproject.org

Galaxy at Bioinformatics Interoperability SIG, ISMB 2012
by Michael Reich 01 Jun '12

01 Jun '12

Dear Galaxy developer community, Galaxy tool developers attending ISMB are encouraged to sign up for the Bioinformatics Interoperability SIG to be held on Friday, June 13. The SIG will include presentations on Galaxy and other interoperability environments and will feature a hackathon where tool developers can add their tools to Galaxy or another environment. For more information about the SIG please see the BSI SIG Web site<http://www.broadinstitute.org/software/bsi-sig/>. Information about ISMB and how to register is at http://www.iscb.org/ismb2012. Sincerely, BSI SIG Committee -- __________________________________________________________ Michael Reich <mreich(a)broadinstitute.org> Director of Cancer Informatics Development Broad Institute of MIT and Harvard 7 Cambridge Center, Cambridge, MA 02142, USA (617) 714-7467 http://www.broadinstitute.org/cancer

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tool shed data type problem?
by Luobin Yang 01 Jun '12

01 Jun '12

Hi, After I update galaxy-dist to the latest version, I got the following error message when I run run.sh command: galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-01 09:57:15,503 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 64, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File "/home/galaxy/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line 26, in load_proprietary_datatypes load_datatype_items( self.app, tool_shed_repository, relative_install_dir ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 1024, in load_datatype_items converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/shed_util.py", line 236, in alter_config_and_load_prorietary_datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) TypeError: load_datatypes() got an unexpected keyword argument 'override'

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June 2012 Galaxy Update
by Dave Clements 01 Jun '12

01 Jun '12

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uploading multiple files into one dataset
by Jorrit Boekel 01 Jun '12

01 Jun '12

Dear list, Our lab's proteomics data is frequently outputted into >50 files containing different fractions of proteins. The files are locally stored and not present on the Galaxy server. We've planned to somehow (inside galaxy) merge these files and split them into tasks so they can be run on the cluster. We would either merge/split the files by concatenation, or untar/tar files at every job, depending on filetype and tool. No problems so far. However, I have been looking around for a way to upload >50 files simultaneously to galaxy and convert to one dataset, and this does not seem to be supported. Before starting to create a hack to make this work, which doesn't seem especially trivial to me, I'd like to know if I should instead use libraries. From what I've seen, libraries are not treated as datasets in Galaxy but rather contain datasets. If there was a "tar all sets in library and import to history" I'd be using that, but I've only encountered "tar/zip sets and download locally" which would be a bit of a workaround. I haven't found much on this subject in the mailing list, has this functionality been requested before? cheers, jorrit boekel

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Problem -> submit job with PBS Torque
by Marc Bras 01 Jun '12

01 Jun '12

Hi !! I've got a problem with PBS when I want to submit a job to our cluster with Galaxy. Every time, PBS says me "pbs_submit failed, PBS error 15023: Bad user - no password entry". Indeed, Galaxy uses my email address (used in Galaxy) as user by default ! But, before, when I used SGE on my previous lab, Galaxy used the galaxy owner user and not my email… Is it possible to set the owner user as previous Galaxy version ? (I found the "drmaa_external_*" session in universe but I don't really understand how to configure this part…). Thanks a lot, Best Regards BRAS Marc

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tool_dependency_dir not being used?
by Ann Black-Ziegelbein 31 May '12

31 May '12

Hi - I have been trying to run a quick test using the tool_dependency_dir configuration option to prove out how it works ... but unfortunately I can't get it to function right. I was hoping someone could point out my error. I have written a simple tool in galaxy, version_test, that will just echo out a version number to a text file so I could test out tool dependencies and install locations. But my required package is not getting resolved by galaxy.... Snippet from my configuration file: # Directory which contains dependent tool binaries or a env.sh to set env vars in order to find specific versions. tool_dependency_dir = /opt My simple tool: <tool id="version_test" name="version_test" version="1.0.0"> <requirements> <requirement type="package">galaxy_test</requirement> </requirements> <description>provides simple stats on BAM files</description> <command>test.sh "$output1" </command> <inputs> <param name="input1" type="data" format="tabular,binary" label="Holder for input file - not used." /> </inputs> <outputs> <data name="output1" format="txt" /> </outputs> </tool> My filesystem: [galaxy@galaxy-0-4:galaxy-dist]$ ls -lat /opt/galaxy_test/ total 20 drwxr-xr-x 3 root root 4096 May 16 14:10 2.0 drwxr-xr-x 3 root root 4096 May 16 14:09 1.0 drwxr-xr-x 4 root root 4096 May 16 14:05 . -rw-r--r-- 1 root root 50 May 16 14:05 env.sh drwxr-xr-x 72 root root 4096 May 16 14:04 .. My env file: #!/bin/bash PATH=/opt/galaxy_test/1.0/bin:$PATH export PATH Galaxy log messages when invoking my test tool: galaxy.tools DEBUG 2012-05-31 21:59:17,349 Dependency galaxy_test galaxy.tools WARNING 2012-05-31 21:59:17,349 Failed to resolve dependency on 'galaxy_test', ignoring If I manually source the env.sh file , my test.sh is found and executes as appropriately. Where am I going wrong? Thanks much! Ann

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Error executing tool: cannot find 'database'
by Marine Rohmer 31 May '12

31 May '12

Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the <command>, <param> etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface. However, when I execute my tool, Galaxy says to me : Error executing tool: cannot find 'database' And in my shell, I can see : 127.0.0.1 - - [30/May/2012:10:47:01 +0200] "GET /tool_runner?tool_id=myTool HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py", line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 333, in execute data.name = fill_template( output.label, context=params ) File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner?tool_id=myTool" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0" I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04) All help will be very very appreciated ! Thank you, Marine

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Galaxy administrators - admin_users setting
by Peter Cock 30 May '12

30 May '12

Hi all, To make someone an administrator on a local Galaxy install, do I just need to add their email (login) to the comma separated setting admin_users in universe_wsgi.ini? https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface I have this working on one server, but it doesn't seem to have any effect on a second server. Both are now running the current release (changeset 50e249442c5a). Is there some other setting needed to enable the admin interface? Thanks, Peter

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Is there a way to turn of the pretty display for VCF files
by Anthonius deBoer 29 May '12

29 May '12

Hi, Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is... Where is this pretty printer and how do I turn it off? Thanks Thon

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starting galaxy server - Paste/egg installation
by Shantanu Pavgi 29 May '12

29 May '12

Hi, Has there been any change in the way galaxy-dist server is started up? I am getting following error after running 'run.sh --daemon' command after galaxy initializes config files from .sample files: {{{ Initializing community_wsgi.ini from community_wsgi.ini.sample Initializing datatypes_conf.xml from datatypes_conf.xml.sample … ... Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Command 'serve' not known (you may need to run setup.py egg_info) No commands registered. Have you installed Paste Script? (try running python setup.py develop) }}} Do I need to install eggs separately using some other script? Any help? -- Shantanu

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