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"
> > in your mail client.  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/
> 
> 



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