- galaxy-dev - lists.galaxyproject.org

Quick question regarding dist and central
by michael burrell (TSL) 20 Sep '11

20 Sep '11

Good afternoon, Just a quick question, is it possible to switch an installed version of galaxy from the central repository to the dist repo? Thanks Michael.

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Galaxy Tool permission/Access
by sohkhan＠notes.cc.sunysb.edu 20 Sep '11

20 Sep '11

Hi, I am wondering if there is way to manage user access to Galaxy tools? I.E, certain users are restricted to use certain tools. Thanks. -Sohail

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Galaxy test quotas
by Candace Seeve 20 Sep '11

20 Sep '11

I've deleted all of my histories and datasets and the status bar in the top right corner indicates that I am using 67% of my quotas. Is there any way to remove all data and jobs to return to 0%? Thanks.

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outputting different numbers of files based on variables?
by Nikhil Joshi 17 Sep '11

17 Sep '11

Hi all, Is it possible to output a different number of files based on variables that the use has chosen? I have a program that will output different numbers of files based upon the input data. So, for example, if the user wants to use a single-end fastq file, the program outputs only one file, however, if the user chooses paired-end fastq files, it outputs three files. Is there any way to get that to work in just one tool? I could make separate tools for single vs. paired end, but I'd rather not. - Nik.

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update for library
by Belinda M. Giardine 17 Sep '11

17 Sep '11

I have the files ready for an update to the Putative SNP phenotypes library. All the new files use hg19 coordinates. They should go either into a new library or put subdirectories under the first where you chose the build. What is the best way to add the metadata to these files? The files are located on draco.bx.psu.edu under /scratch/giardine/galaxyLib/. As I work on a poster for the ASHG and HGVS meetings I may think of more files to add. Belinda

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DeFuse gene fusion detection tool added to toolshed
by Jim Johnson 17 Sep '11

17 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 17 Sep '11

17 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 17 Sep '11

17 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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