Hi Bjoern,
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/000/101
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/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_settings/GATK2_PATH/iuc/gatk2/8bcc13094767;
exp
ort PACKAGE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc
c13094767/env.sh;
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_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
${GALAXY_SLOTS:-4} -R ""
'; return_code=$?; 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/000/101 .
/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_102_DXIvP5,/software/packages/galaxy/galaxy-dis
t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax
y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac
kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK
a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso
ciation_102__IZJ7Y
/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD
atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k
wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-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,,/software/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
>
>
>
>
> ___________________________________________________________
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