September 2011 - galaxy-dev - lists.galaxyproject.org

DeFuse gene fusion detection tool added to toolshed
by Jim Johnson 16 Sep '11

16 Sep '11

I added a defuse galaxy tool to the toolshed: http://toolshed.g2.bx.psu.edu/ DeFuse is software developed by Andrew McPherson for gene fusion discovery using RNA-Seq data. http://sourceforge.net/projects/defuse/

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Running a new installation of Galaxy on a high performance computer cluster
by David Matthews 16 Sep '11

16 Sep '11

Hi, We are getting ready to run a local setup of Galaxy here at bristol university on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and now we want to install it properly on the main cluster and have the galaxy instance run in the queue along with all the other HOC jobs that are submitted to BlueCrystal from around the university. The guy doing the install has just sent me this message: When I add the following line: database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy to universe_wsgi.ini Galaxy fails to start with the following error message: snip ---------------------- galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line 33, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 105, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '76' but this code expects version '81'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. postgres on the web server is 8.4 so it should be fine. It looks like python is reporting the wrong version number. Any help from the developers would be much appreciated. Do you know what the problem is he is seeing? Would he be better off emailing you directly? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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Export galaxy interval data to InterMine
by Fengyuan Hu 16 Sep '11

16 Sep '11

Dear Galaxy developers, I'm trying to create a tool to export galaxy interval data to InterMine instances. Firstly, based on the tool to send dataset to EpiGRAPH, I created one to FlyMine, it's working on my local instance. Then I tried a bit complex one, to integrate multiple mines in one tool, source xml as following: <?xml version="1.0"?> <tool name="Perform advanced genomic region search" id="intermine_export"> <description> with an InterMine instance</description> <redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name} INFO=${input1.info}</redirect_url_params> <inputs> <param format="bed" name="input1" type="data" label="Send this dataset to an InterMine instance"> <validator type="unspecified_build" /> </param> <conditional name="destination"> <param name="indexDestination" type="select" label="Select InterMine instance" help="InterMine genomic region search service."> <option value="flymine">FlyMine</option> <option value="modmine">modMine</option> <option value="metabolicmine">MetabolicMine</option> </param> <when value="flymine"> <param name="REDIRECT_URL" type="hidden" value="http://www.flymine.org/query/genomicRegionSearch.do" /> </when> <when value="modmine"> <param name="REDIRECT_URL" type="hidden" value="http://intermine.modencode.org/query/genomicRegionSearch.do" /> </when> <when value="metabolicmine"> <param name="REDIRECT_URL" type="hidden" value="http://www.metabolicmine.org/beta/query/genomicRegionSearch.do" /> </when> </conditional> <param name="DATA_URL" type="baseurl" value="/datasets" /> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=intermine_import" /> </inputs> <outputs/> <help> some help text here... </help> </tool> I use <conditional> tag on intermine instances, it will be parsed to a dropdown list in html page, every time I select a different mine, I'd like the value of "REDIRECT_URL" param to change accordingly, but this is not working. After testing and reading the doc a bit, I realised that "REDIRECT_URL" will be renamed "destination | REDIRECT_URL" in the rendered html, and the xml parser will only recognise the key word "REDIRECT_URL" (reserved), is this the case? Can I still valid my logics in the xml? Thanks Fengyuan

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uploading binary files checksum changes, Galaxy doing something to file?
by Leandro Hermida 16 Sep '11

16 Sep '11

Hi all, We tried to find something in the docs and mailing list no luck. We created a new datatype the is a straight subclass of Binary and then when we upload such a file in the Galaxy UI and check the checksums between the original file and the file located in the Galaxy database/files/... directory their checksums are different! What are we doing wrong? We simply want Galaxy to upload and no touch the file at all. regards, Leandro

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Re: [galaxy-dev] GATK Unified Genotyper
by Chorny, Ilya 16 Sep '11

16 Sep '11

Hi Daniel, I have been implementing the GATK unified genotyper and I was having some issues. Occasionally I would get an error that the Java virtual machine would not start. I got around that by adding the Xmx3g parameter to the command line. I also added the -nt 3 because otherwise it's really slow on human data. --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index #end for -p 'java -Xmx3g -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" -o "${output_vcf}" ##-o "out_vcf.txt" -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if -nt 3 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Setting the output label based on input parameters?
by Nikhil Joshi 16 Sep '11

16 Sep '11

Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik.

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redirecting sdterr
by Mikel Egaña Aranguren 16 Sep '11

16 Sep '11

Hi; I'm sure this has been mentioned before but perhaps it has been fixed. I'm writting a wrapper of a Java tool for Galaxy. The tool throws info to stderr even when working properly, and Galaxy interprets it as a bug. Is there any way of redirecting stderr (It seems that normal UNIX redirection to a file does not work) or making Galaxy ignore it? Thanks -- Mikel Egaña Aranguren, PhD http://mikeleganaaranguren.com Marie Curie post-doc at Ontology Engineering Group, UPM http://www.oeg-upm.net/

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optional integer value in tool config
by Sarah Diehl 15 Sep '11

15 Sep '11

Hello, in the config of a tool I want to integrate into Galaxy I would like to have a parameter with the following properties: <param name="var" type="integer" label="Var" value="50" optional="true" min="10" max="100" /> So it should be possible to leave this field empty, but when you choose to enter a number it should be between 10 and 100. The problem now is that Galaxy refuses to accept it when this field is empty. After encountering this problem I tried to solve the issue within Cheetah and tried the following: #if $var.value < 10 or $var.value > 100 #set $var.value = "" #end if Galaxy however throws the following error when loading the tool: galaxy.tools ERROR 2011-07-04 14:04:14,231 error reading tool from path: path/to/tool.xml Traceback (most recent call last): File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/galaxy/galaxy_server/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 583, in parse parser.feed(data) File "/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1242, in feed self._parser.Parse(data, 0) ExpatError: not well-formed (invalid token): line 230, column 21 The token it is complaining about is the <. I searched the Cheetah documentation and also Google but was not able to come up with a solution. Could anyone of you knowledgeable guys help me find a solution to this, please? I would be very grateful! Thanks in advance! Best regards, Sarah

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Re: [galaxy-dev] [galaxy-user] galaxy test-data organization
by Jennifer Jackson 15 Sep '11

15 Sep '11

> To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > You will want to choose one or both of these: http://lists.bx.psu.edu/listinfo/galaxy-user http://lists.bx.psu.edu/listinfo/galaxy-dev -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Re: [galaxy-dev] [galaxy-user] galaxy test-data organization
by Jennifer Jackson 15 Sep '11

15 Sep '11

Hello Joe, Functional test-data is located here in the source: http://bitbucket.org/galaxy/galaxy-central/src/07c5fbd618f3/test-data/ The name/comments of each is the best way to understand the link between a test and a tool (could be many-to-many). Next time, a question like this about a local instance would be better directed to the galaxy-dev(a)bx.psu.edu mailing list, so I am going to forward this there. There is an active user community, perhaps someone has organized the functional test data in a different other way for their own purposes and would like to share the method. Thanks for using Galaxy! Best, Jen Galaxy team On 8/27/11 7:17 AM, Joseph Hargitai wrote: > ===> Please use "Reply All" when responding to this email!<=== > > > > > > Hi, > > is there by any chance a per application breakdown of the test-data > structure? > > best, > joe > > > > ___________________________________________________________ > 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 Jackson http://usegalaxy.org http://galaxyproject.org/Support

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