February 2013 - galaxy-dev - lists.galaxyproject.org

Tool wrapper XSD
by Pierre Pericard 21 Feb '13

21 Feb '13

Hi everyone, Is there a Galaxy XML tool wrapper XSD ? Thanks, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/

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Re: [galaxy-dev] KeyError ['tools'] on importing workflow from locally installed repository
by jorrit poelen 21 Feb '13

21 Feb '13

Hi Dave, Thanks for the quick reply. Your fix worked like a charm! -jorrit > Date: Tue, 19 Feb 2013 12:54:23 -0500 > From: Dave Bouvier <dave(a)bx.psu.edu> > To: galaxy-dev(a)lists.bx.psu.edu, closeticket(a)galaxyproject.org > Subject: Re: [galaxy-dev] KeyError ['tools'] on importing workflow > from locally installed repository > Message-ID: <5123BC4F.90500(a)bx.psu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Jorrit, > > Thank you for uncovering that issue, I've commited a fix in the stable > branch of galaxy-central at 8887:d5896e8a60fa. To apply that changeset, > you'll need to run the following commands from your Galaxy directory: > > $ hg pull -b stable https://bitbucket.org/galaxy/galaxy-central/ > $ hg update stable > > --Dave B. > > On 2/18/13 21:57:18.000, jorrit poelen wrote: >> Hey y'all, >> >> I am testing how to best share a workflow through a tool shed. I stumbled across a possible bug and am hoping that this is simply a configuration issue. >> >> Steps to reproduce: >> >> 1. In local galaxy instance goto . . admin > search and browse tool sheds >> 2. locate select "Galaxy test tool shed" >> 3. search for "obo" >> 4. preview and install repository "obo_test_workflows" >> 5. in next screen click "install to Galaxy" >> 6. in next screen click "install" >> 7. in next screen click "obo_test_workflows" >> 8. in next screen, under workflows, click "TestOboWorkflow1" >> 9. in svg graphics page > repository actions > import workflow to galaxy >> >> Expected results: >> Workflow is installed and made available in workflow section in local Galaxy instance. >> >> Actual results: >> URL: http://galaxy:7474/admin_toolshed/import_workflow?repository_id=2d9035b3fc1… >> File '/home/ubuntu/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond >> app_iter = self.application(environ, detect_start_response) >> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ >> environ, self.app) >> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output >> app_iter = application(environ, replacement_start_response) >> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ >> return self.application(environ, start_response) >> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ >> return self.application(environ, start_response) >> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ >> return self.handle_request( environ, start_response ) >> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request >> body = method( trans, **kwargs ) >> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 216 in decorator >> return func( self, trans, *args, **kwargs ) >> File '/home/ubuntu/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 744 in import_workflow >> tools_metadata = metadata[ 'tools' ] >> KeyError: 'tools' >> >> Thanks in advance for suggestions on how to solve / work around this issue. >> >> -jorrit >> >> PS Note that the workflow can be installed using a url pointing to the workflow from a hg repository on bitbucket (ie. https://bitbucket.org/jhpoelen/obo_workflows/raw/25d386a50562d02e03fa821d96…) >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> > >

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New release : display problem
by Mathieu Bahin 21 Feb '13

21 Feb '13

Hi there, I am using my own Galaxy instance and since I updated, I can't see file of several datatypes (for example the 'tabular' ) clicking on the eye icon. Is that a problem linked to the new release ? Cheers, Mathieu Bahin

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where to announce transcript annotation file in local Galaxy install
by Maxim 21 Feb '13

21 Feb '13

Hi, I got my local instance of Galaxy running and most tools work properly. Unfortunately I seem not to understand how to implement cufflinks within Galaxy, in particular I do not know how to inform Galaxy about the location of GTF annotation files. I searched the archives for this and was not successful. Furthermore I cannot find a preference file holding cufflinks specific information nor a general place to keep annotation data. Who can point me there? Best regards and thanks for your effort! Maxim

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tophat for illumina looking in wrong directory for bowtie2 indexes?
by greg 21 Feb '13

21 Feb '13

Hi guys, I'm getting this error when running tophat for Illumina: Error in tophat: [2013-02-20 16:43:50] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2013-02-20 16:43:50] Checking for Bowtie Bowtie version: 2.0.2.0 [2013-02-20 16:43:50] Checking for Samtools [2013-02-20 16:43:50] samtools_path: None [2013-02-20 16:43:50] samtools_path after prog_path: /usr/local/galaxy/installs/bin/samtools-0.1.18/samtools Samtools version: 0.1.18.0 [2013-02-20 16:43:50] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex.*.bt2) But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file: mm10 mm10 mm10 /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index Why isn't it looking in that directory for the bowtie2 files? It's almost as if it's reading my bowtie_indices.loc file instead? Thanks, Greg

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Problem with saving workflows
by Alexander Kurze 21 Feb '13

21 Feb '13

Hello, I am running a local server of Galaxy. I have a problem with editing and then saving already created workflows. The "saving workflow" bar just does not disappear anymore. I can hit the save on an unaltered workflow, the saving workflow bar appears for 2 secs and then it disappears how it should do. Does anyone now how I can fix it? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341

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Error when trying to display data on gene track
by Perez, Ricardo 21 Feb '13

21 Feb '13

Hello, We are running a local instance of galaxy and we get the following error when trying to display genes from our history in the ucsc browser. I got the error as I was following the galaxy 101 video in the galaxy website (last step). Thanks, --Ricardo Perez URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=ge… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application >> display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link >> return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ >> self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict >> if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready >> raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file extra data full traceback URL: http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=ge… Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application >> display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link >> return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ >> self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict >> if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready >> raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file

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FastQC Question
by Min Cho 21 Feb '13

21 Feb '13

Hello, When trying to run FastQC, I get this error: Traceback (most recent call last): File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 162, in <module> html,retval,serr = f.run_fastqc() File "/home/bal/galaxy-dist/tools/rgenetics/rgFastQC.py", line 63, in run_fastqc sout.write('# FastQC cl = \n' % ' '.join(cl)) TypeError: not all arguments converted during string formatting Is there anything I can do to modify the code to fix this? I'm using data run through FASTQ Groomer. Thank you

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dynamic select problem
by Smithies, Russell 20 Feb '13

20 Feb '13

I've been tweaking the blast+ tool xml to simplify database selection for our users (we have a lot of databases) and have made it multi-tiered through the use of two select boxen and a filter. Basically, I've added an extra column to blastdb.loc with a group name, then use this as a filter to only display the group of databases that were chosen in the top select. Surprisingly it works - but I doubt it was the intention of the devs who wrote the filter code! But there's a small bug that I can't see, the selects work correctly but I get a warning on the secondary one "An invalid option was selected, please verify" Any ideas what I've overlooked? Ideally I'd like to only read the file once and load into a data structure then populate the second select based on the choice from the top one - but that may be asking too much from Cheetah and Galaxy? Thanx, --Russell My select code looks like this: <param name="db_type_select" type="select" label="Subject database type"> <options from_file="blastdb.loc.4col"> <column name="value" index="3"/> <column name="name" index="3"/> <filter type="unique_value" name="name" column="3" /> <filter type="sort_by" name="name" column="3" /> </options> </param> <param name="species_select" type="select" label="Database name"> <options from_file="blastdb.loc.4col"> <column name="value" index="0"/> <column name="name" index="1"/> <column name="path" index="2"/> <filter type="param_value" ref="db_type_select" column="3"/> </options> </param> This is an example of the extra column added to blastdb.loc: agall.seq All AgResearch ESTs /dataset/blastdata/active/species/agall.seq AgR Databases agruminant_plus.seq All AgResearch Ruminant ESTs, plus NCBI public Bos Taurus as at 3/2002, plus NCBI Sheep at 7/2002 /dataset/blastdata/active/species/agruminant_plus.seq Ruminant Databases galaxy-dev@inconstant$ head -n20 ../../tool-data/blastdb.loc.4col arrayprinturg15k.seq 15Kurg (ESTs) /dataset/blastdata/active/species/arrayprinturg15k.seq Microarray Databases 454AllContigs.fna 454 Seqs 20/5/2007 /dataset/blastdata/active/species/454AllContigs.fna Sheep Databases AffyBovineArray052006.seq Affy Bovine Array at 5/2006 /dataset/blastdata/active/species/AffyBovineArray052006.seq Cattle Databases AFT_Affy_chip_seqs.fa AFT Affy Array 6/2006 /dataset/blastdata/active/species/AFT_Affy_chip_seqs.fa Fungal Databases agilent_mouse Agilent Mouse Array 012694 (as at 2/2007) /dataset/blastdata/active/species/agilent_mouse Rodent Databases est all public ESTs /dataset/blastdata/active/species/est Pub Databases est_others all "other" public ESTs (other than Human Databases, mouse) /dataset/blastdata/active/species/est_others Pub Databases agall_plus.seq All AgResearch ESTs, plus NCBI public Bos Taurus as at 3/2002, plus NCBI Sheep at 7/2002 /dataset/blastdata/active/species/agall_plus.seq AgR Databases agall.seq All AgResearch ESTs /dataset/blastdata/active/species/agall.seq AgR Databases agruminant_plus.seq All AgResearch Ruminant ESTs, plus NCBI public Bos Taurus as at 3/2002, plus NCBI Sheep at 7/2002 /dataset/blastdata/active/species/agruminant_plus.seq Ruminant Databases agruminant.seq All AgResearch Ruminant ESTs /dataset/blastdata/active/species/agruminant.seq Ruminant Databases build2_allssr.seq All BT2.0 SSRs /dataset/blastdata/active/species/build2_allssr.seq Cattle Databases Allium_cepa Allium cepa DFCI gene indices /dataset/blastdata/active/species/Allium_cepa Plant Databases angrep.ref angrep.ref /dataset/blastdata/active/species/angrep.ref Repeat Databases fungalnucs_AR3018_454 AR3018 454 reads, trimmed, 12/2009 /dataset/blastdata/active/species/fungalnucs_AR3018_454 Fungal Databases fungalnucs_AR3018_454ContigsNewbler2.0 AR3018 454 build, 12/2009 /dataset/blastdata/active/species/fungalnucs_AR3018_454ContigsNewbler2.0 Fungal Databases -- ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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Tool wrappers - Triggering warnings on specific options?
by Peter Cock 20 Feb '13

20 Feb '13

Hello all, I was wondering if anyone else writing Galaxy tools has wanted to be able to show warning messages conditional on tool options? For example, setting a parameter to a deprecated value could trigger a warning message (with an OK/Cancel dialogue to allow continuation or returning to the tool options). More generally, a warning might be desirable only if certain options are used together. Even stricter, for some tools it would be useful to show an error message with particular option combinations, and refuse to submit the job. Any thoughts? Peter

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