Mercurial > repos > elixir-it > mutect2
changeset 10:e3662508ee26 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Sun, 22 Sep 2019 16:31:11 -0400 |
| parents | a517190d2b3d |
| children | 057bce4b4f93 |
| files | mutect2.xml mv_untar_gatk.sh |
| diffstat | 2 files changed, 15 insertions(+), 4 deletions(-) [+] |
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--- a/mutect2.xml Sat Sep 21 13:21:54 2019 -0400 +++ b/mutect2.xml Sun Sep 22 16:31:11 2019 -0400 @@ -41,10 +41,11 @@ java -jar \$CONDA_PREFIX/share/picard-2.7.1-2/picard.jar CreateSequenceDictionary R= genome.fa O= genome.dict 2>$log && #end if - ##TODO gatk-register take the GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 unzip it - ##and move the .jar file to \$CONDA_PREFIX/opt/gatk-3.8/ then the mutect2 command is runned - gatk3-register \$_CONDA_DIR/../GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 2>$log ; - java -jar \$CONDA_PREFIX/opt/gatk-3.8/GenomeAnalysisTK.jar -nct 4 -T MuTect2 -I:tumor tumor.bam -I:normal normal.bam -o $output + ##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 && + + 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" -R genome.fa #end if
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mv_untar_gatk.sh Sun Sep 22 16:31:11 2019 -0400 @@ -0,0 +1,10 @@ +#!/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 + tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar + +else + echo GATK is present +fi +