Remove unused sh

snakecnv/bin/gstrip_preprocess.sh

-#!/bin/bash
-
-# If you adapt this script for your own use, you will need to set these two variables based on your environment.
-# SV_DIR is the installation directory for SVToolkit - it must be an exported environment variable.
-# SV_TMPDIR is a directory for writing temp files, which may be large if you have a large data set.
-# export SV_DIR=/usr/local/bioinfo/src/genomeSTRIP/svtoolkit
-
-echo "---"
-echo "Running gstrip_preprocess.sh $1 $2 $3 $4 $5"
-echo "Starting "`date +%Y-%m-%d`" at "`date +%H:%M:%S`
-echo "---"
-
-myname=`basename "$0"`
-
-function usage() {
-    echo "
-Program: SVpreprocess wrapper
-usage:   $myname  <bamlist> <gendermap> <genome> <outdir> <outprefix>
-
-positional args:
-        bamlist    a file listing the bamfiles
-        gendermap  the gendermap file for genomestrip
-        genome     the genome fasta file (the genomestrip reference genome fasta file)
-        outdir     output directory
-        outprefix  prefix for the run directory
-"
-}
-
-bamlist=$1
-gendermap=$2
-genome=$3
-outdir=$4
-outprefix=$5
-
-if [[ -z ${bamlist} || -z ${gendermap} || -z ${genome} || -z ${outdir} || -z ${outprefix} ]]
-then
-   usage
-   echo "At least one argument is missing"
-   exit 1
-fi
-
-inputFile=$bamlist
-reference_prefix=${genome%.fasta}
-
-runDir=${outdir}/${outprefix}_run
-SV_TMPDIR=${outdir}/${outprefix}_tmp
-
-# For SVAltAlign, you must use the version of bwa compatible with Genome STRiP.
-export PATH=${SV_DIR}/bwa:${PATH}
-export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
-
-mx="-Xmx4g"
-classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
-
-echo $classpath
-
-mkdir -p ${SV_TMPDIR}
-mkdir -p ${runDir}/logs || exit 1
-mkdir -p ${runDir}/metadata || exit 1
-
-# Display version information.
-java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar
-
-echo "-- Run Preprocessing -- "
-# Run preprocessing.
-export LD_LIBRARY_PATH=/SGE/ogs/lib/linux-x64:$LD_LIBRARY_PATH
-classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
-
-if [ -n "$SV_PARALLEL_DRMAA" ] && [ "$SV_PARALLEL_DRMAA" -eq "1" ]; then
-
-LC_ALL=C java -Xmx4g -cp ${classpath} \
-      org.broadinstitute.gatk.queue.QCommandLine \
-     -S ${SV_DIR}/qscript/SVPreprocess.q \
-     -S ${SV_DIR}/qscript/SVQScript.q \
-     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-     -cp ${classpath} \
-     -jobProject Capri \
-     -jobRunner Drmaa \
-     -gatkJobRunner Drmaa \
-     -jobQueue workq \
-     -jobNative "${SV_PARALLEL_NATIVES}" \
-     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-     -tempDir ${SV_TMPDIR} \
-     -R ${reference_prefix}.fasta \
-     -I ${inputFile} \
-     -runDirectory ${runDir} \
-     -md ${runDir}/metadata \
-     -jobLogDir ${runDir}/logs \
-     -disableGATKTraversal \
-     -bamFilesAreDisjoint true \
-     -computeGCProfiles  true \
-     -computeReadCounts  true \
-     -copyNumberMaskFile ${reference_prefix}.gcmask.fasta \
-     -genderMaskBedFile  ${reference_prefix}.gendermask.bed \
-     -genomeMaskFile     ${reference_prefix}.svmask.fasta \
-     -ploidyMapFile      ${reference_prefix}.ploidymap.txt \
-     -readDepthMaskFile  ${reference_prefix}.rdmask.bed \
-     -genderMapFile      ${gendermap} \
-     -maxConcurrentRun 20 \
-     -run \
-     || exit 1
-
-else
-
-LC_ALL=C java -Xmx4g -cp ${classpath} \
-      org.broadinstitute.gatk.queue.QCommandLine \
-     -S ${SV_DIR}/qscript/SVPreprocess.q \
-     -S ${SV_DIR}/qscript/SVQScript.q \
-     -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-     -cp ${classpath} \
-     -jobProject Capri \
-     -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-     -tempDir ${SV_TMPDIR} \
-     -R ${reference_prefix}.fasta \
-     -I ${inputFile} \
-     -runDirectory ${runDir} \
-     -md ${runDir}/metadata \
-     -jobLogDir ${runDir}/logs \
-     -disableGATKTraversal \
-     -bamFilesAreDisjoint true \
-     -computeGCProfiles  true \
-     -computeReadCounts  true \
-     -copyNumberMaskFile ${reference_prefix}.gcmask.fasta \
-     -genderMaskBedFile  ${reference_prefix}.gendermask.bed \
-     -genomeMaskFile     ${reference_prefix}.svmask.fasta \
-     -ploidyMapFile      ${reference_prefix}.ploidymap.txt \
-     -readDepthMaskFile  ${reference_prefix}.rdmask.bed \
-     -genderMapFile      ${gendermap} \
-     -run \
-     || exit 1
-
-fi
-
-rm -fr ${SV_TMPDIR}
-mv ${runDir}/metadata ${outdir}/
-
-echo "Script SVPreprocess completed successfully "`date +%Y-%m-%d`" at "`date +%H:%M:%S`