I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think
you habe hg19 as dbkey, otherwise you would not see the hg19 in the select
box. There must be something wrong in you *.log file.


2014-01-30 Briand, Sheldon <sheldon.bri...@ssc-spc.gc.ca>:

>
> We do see hg19 in the reference genome box.  We are using revision
> 8bcc13094767 of the GATK2 wrapper.  The only line in the .loc file is the
> one listed in my first email.  I've put that line in both tool-data and
> tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files.
> We didn't see the reference genome hg19 until the loc file for the repo was
> populated.
>
> Thanks!
> -Sheldon
>
>
>
> -----Original Message-----
> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
> Sent: Thursday, January 30, 2014 1:33 PM
> To: Briand, Sheldon
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] GATK2
>
> Hi Sheldon,
>
> > The loc file is tabular.  I put the 2bit file in the directory and had
> no success.  Here is the rather lengthy commandline:
> >
> > #!/bin/sh
> >
> > export GALAXY_SLOTS_CONFIGURED="1"
> > if [ -n "$SLURM_JOB_NUM_NODES" ]; then
> >     GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> > elif [ -n "$NSLOTS" ]; then
> >     GALAXY_SLOTS="$NSLOTS"
> > elif [ -f "$PBS_NODEFILE" ]; then
> >     GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
> >     GALAXY_SLOTS="1"
> >     unset GALAXY_SLOTS_CONFIGURED
> > fi
> >
> > export GALAXY_SLOTS
> > GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> > if [ "$GALAXY_LIB" != "None" ]; then
> >     if [ -n "$PYTHONPATH" ]; then
> >         PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> >     else
> >         PYTHONPATH="$GALAXY_LIB"
> >     fi
> >     export PYTHONPATH
> > fi
> >
> > [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> > /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> > 00/101
> > PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> > ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> > /gatk2/8bcc13094767/env.sh; PACKAGE
> > _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> > ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> > s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> > PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> > nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> > PACKAGE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/environment_
> > settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
> /software/packages/galaxy/shed_tools/toolshed.g2.b
> > x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py
> --stdout "/software/packages/galaxy/galaxy-dist/da
> > tabase/files/000/dataset_126.dat"     -d "-I"
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> > dat" "bam" "gatk_input"         -d ""
> "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> > data_19.dat" "bam_index" "gatk_input"      -p '          java -jar
> "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "Rea
> > lignerTargetCreator"     -o
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
>      $GATK2_S
> > ITE_OPTIONS      --num_cpu_threads_per_data_thread 1
> --num_threads ${GALAXY_SLOTS:-4}
>
>
> >  -R ""
>
> -> that is the error. Here needs to be your path to the fasta file. Can
> you point to me to Tool Shed Version you are using and are you running the
> latest revision? Do you see hg19 / hg18 in the select-box under
> "using-reference genome"
>
> Can you attach your gatk2_picard_index.loc?
>
> Thanks,
> Bjoern
>
> >
> >  '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> > /software/packages/galaxy/galaxy-dist/set_metadata.sh
> > ./database/files
> > /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> > 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> > /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> > /software/packages/
> > galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> > /software/packages/galaxy/galaxy-dist/database
> > /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
> > 02_DXIvP5,/software/packages/galaxy/galaxy-dis
> > t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
> > ssociation_102_ifJAbu,/software/packages/galax
> > y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
> > oryDatasetAssociation_102_Ie2O0C,/software/pac
> > kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
> > ta_results_HistoryDatasetAssociation_102_xLNtK
> > a,,/software/packages/galaxy/galaxy-dist/database/job_working_director
> > y/000/101/metadata_override_HistoryDatasetAsso
> > ciation_102__IZJ7Y
> > /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> > 00/101/metadata_in_HistoryD
> > atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat
> > abase/job_working_directory/000/101/metadata_k
> > wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/gal
> > axy-dist/database/job_working_directory/000/10
> > 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages
> > /galaxy/galaxy-dist/database/job_working_direc
> > tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/s
> > oftware/packages/galaxy/galaxy-dist/database/j
> >
> ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY;
> sh -c "exit $return_code"
> > echo $? > /software/packages/galaxy/galaxy-dist/database/pbs/101.ec
> >
> > Thanks,
> > -Sheldon
> >
> > -----Original Message-----
> > From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
> > Sent: Thursday, January 30, 2014 12:26 PM
> > To: Briand, Sheldon
> > Cc: galaxy-dev@lists.bx.psu.edu
> > Subject: Re: [galaxy-dev] GATK2
> >
> > Hi,
> >
> > do you have access to the generated commandline from Galaxy and can
> paste it her?
> >
> > >
> > > I've installed the latest version (using GATK2.8-1) of the GATK2
> > > wrapper here.  I've run into the following error:
> > >
> > > ##### ERROR MESSAGE: The fasta file you specified
> > > (/tmp/tmp-gatk-V7IrBw) does not exist.
> > >
> > >
> > >
> > > I see via much googling that this error is due to a user input
> > > problem.  I've tried pointing the gatk2_picard_index.loc file in
> > > tool-data to the proper data files:
> > >
> > > hg19 hg19    hg19    /software/packages/galaxy/data/picard/hg19.fa
> >
> > That look ok, as far as every token is separated by a tabular.
> >
> > >
> > > where the following files exist:
> > >
> > > hg19.dict
> > >
> > > hg19.fa
> > >
> > > hg19.fa.fai
> >
> > Can you put the 2bit file into the same folder?
> >
> > Cheers,
> > Bjoern
> >
> >
> > >
> > > I'm using a torque setup.  A bam file is being used as input.  After
> > > much trial and error I've been unable to figure out what I'm missing.
> > >
> > >
> > >
> > > None of the solutions on google apply to my situation.
> > >
> > >
> > >
> > > Has anyone else run into this configuration problem and solved it?
> > >
> > >
> > >
> > > Thanks,
> > >
> > > -Sheldon
> > >
> > >
> > >
> > > Sheldon Briand
> > >
> > > NRC Research Computing Support Analyst
> > >
> > > Research Computing Support / Soutien Informartique a la Recherche
> > >
> > > Operations, Science Portfolio / Operations, Portefeuil des sciences
> > >
> > > SSC-NRC / SPC-CNRC
> > >
> > > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> > >
> > > Halifax, NS  B3H 3Z1
> > >
> > > 902 426-1677
> > >
> > > sheldon.bri...@ssc-spc.gc.ca
> > >
> > >
> > >
> > >
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
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> > >
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> >
> >
>
>
>
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