- galaxy-dev - lists.galaxyproject.org

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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Finding cruft in database/files/?
by Brian Claywell 25 Mar '14

25 Mar '14

Is there an existing method for finding files in $GALAXY_DIR/database/files that have been orphaned due to errors, or leftover from testing, etc? I'm pretty sure ours is bigger than it ought to be, and I'd really like to look at a little audit of the files there vs the ones registered in Galaxy. Thanks! -- Brian Claywell, Systems Analyst/Programmer Fred Hutchinson Cancer Research Center bclaywel(a)fhcrc.org

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Forward of moderated message
by galaxy-user-bounces＠lists.bx.psu.edu 25 Mar '14

25 Mar '14

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Error running worflows from the ToolShed
by Björn Grüning 24 Mar '14

24 Mar '14

Hi, anyone saw that error already and has a fix or workaround? It happens with: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow http://toolshed.g2.bx.psu.edu/view/galaxyp/proteomics_rnaseq_splice_db_work… Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'iteritems' URL: http://galaxy.uni-freiburg.de/workflow/load_workflow?id=a1f33a6ea049e40d&_=… File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 78 in decorator return to_json_string( func( self, trans, *args, **kwargs ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 686 in load_workflow module = module_factory.from_workflow_step( trans, step ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 443 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 251 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2421 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 98 in params_from_strings for key, value in param_values.iteritems(): AttributeError: 'NoneType' object has no attribute 'iteritems' Cheers, Bjoern

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Suppress stdout in history item
by Hans van Leeuwen 24 Mar '14

24 Mar '14

Hi, Currently if there is anything written to stdout it is also shown in the expanded history item of the job (in the right hand history panel). Is there a way to suppress that? I searched for a possible solution but could not find anything. Thank you, Best regards, Hans van Leeuwen

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trackster problem for version-2014.02.10
by Shu-Yi Su 23 Mar '14

23 Mar '14

Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. "GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245&hda_ldda=hda The log where the trackster is working (from the old installation): 1. "GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6&hda_ldda=hda…… 2. "GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hda&data_type=converted_datasets_state…. 3. "GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=data&chrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked "View in new visualization" (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi

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migrate to postgresql
by Jun Fan 23 Mar '14

23 Mar '14

Hi all, I followed the instruction on https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and managed to migrate to a postgresql on a Ubuntu machine. However when I tried on a CentOS 6.5, it failed.The steps are: 1. Create psql user galaxy: under psql prompt, a. CREATE USER galaxy WITH PASSWORD 'galaxy'; b. CREATE DATABASE galaxy; c. GRANT ALL PRIVILEGES ON DATABASE galaxy to galaxy; 2. test the created account: change authentication method to password in pg_hba.conf and the username/password works 3. add postgresql://galaxy:galaxy@localhost/galaxy to universal_wsgi.ini 4. sh run.sh gave me the error saying FATAL: Ident authentication failed for user "galaxy" 5. even I changed back to the default IDENT authentication for postgresql in pg_hba.conf, the same error message appeared. Could anyone help me to spot the error here? Best regards! Jun

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Common workflow test tools
by Ravi Alla 22 Mar '14

22 Mar '14

Hello galaxy community, I have a question regarding testing tools. I just setup a galaxy server to submit jobs to a cluster. Everything seems to be in order so far. Are there established workflows with test data that allow you to test a typical analysis (ex. RNA-Seq - from raw reads to counts, ChIP-Seq-from raw reads to enriched regions, SNP analysis-from raw reads to a VCF file etc). I want to be able run my tools on small test sets to make sure everything is fine and dandy, before I open it up to some beta testers. As an aside does galaxy have any dataset size limitations? Does it work equally well with an 8GB fastq/bam file compared to a 50-100GB fastq/bam? Thanks Ravi

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Output file to history
by Jennifer Jackson 22 Mar '14

22 Mar '14

Hi Sebastian, I'm going to move this over to the galaxy-dev(a)bx.psu.edu mailing list so that it reaches the development community effectively. I personally do not know the answer, but I am sure we can get you some help. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists On 3/21/14 9:28 AM, Sebastian Luna Valero wrote: > > Dear All, > > I am trying to add a new tool in Galaxy and I have the following problem. > > Let me explain a simplified example. Let's imagine that my script > works from CLI as follows: > > python script.py --input "input-file" --pattern "output-pattern" > > After processing "input-file", the script writes several output files > and their name is given according to "output-pattern". > > The number of output files depends on the content of "input-file". The > output files are written to the current working directory where > script.py is located. > > In the simplest scenario, I get only one output file in the working > directory. > > My problem is that I would like to see the output files in Galaxy's > history without modifying the CLI interface. > > To solve this problem, I have looked at the wiki page: > > https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number… > > and the email here: > > http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-hi… > > However, I think that mine is a different scenario. I do not want to > add new output parameters in the CLI. I would like Galaxy to bring > these output files to my history without modifying the CLI options, is > that possible? > > Many thanks in advance for your help! > > Best regards, > Sebastian. > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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blast+ wrapper with remote searching
by Nilaksha Neththikumara 21 Mar '14

21 Mar '14

Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha

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