Mercurial > repos > elixir-it > mutect2
changeset 11:057bce4b4f93 draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Wed, 02 Oct 2019 04:39:04 -0400 |
| parents | e3662508ee26 |
| children | |
| files | mutect2.xml mv_untar_gatk.sh |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/mutect2.xml Sun Sep 22 16:31:11 2019 -0400 +++ b/mutect2.xml Wed Oct 02 04:39:04 2019 -0400 @@ -43,7 +43,7 @@ ##TODO gatk mv_untar_gatk take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it ##and move .jar and command is runned - sh $__tool_directory__/mv_untar_gatk.sh && + bash $__tool_directory__/mv_untar_gatk.sh &> $log && java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output #if $reference_source.reference_source_selector == "history"
--- a/mv_untar_gatk.sh Sun Sep 22 16:31:11 2019 -0400 +++ b/mv_untar_gatk.sh Wed Oct 02 04:39:04 2019 -0400 @@ -1,7 +1,7 @@ #!/bin/bash #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm #and untar the archive -if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then +if [ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ] ; then tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar else