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Checking for key executables #3

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Checking for key executables #3

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12 changes: 12 additions & 0 deletions scripts/prepReference.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -135,6 +135,10 @@ if [[ "$SnpPipeline_Aligner" == "" || "$SnpPipeline_Aligner" == "bowtie2" ]]; th
if [[ $opt_f_set != "1" && -s "$referenceBasePath.rev.1.bt2" && "$referenceBasePath.rev.1.bt2" -nt "$referenceFilePath" ]]; then
echo "# Bowtie index $referenceBasePath.rev.1.bt2 is already freshly built. Use the -f option to force a rebuild."
else
if [[ "$(which bowtie2-build >/dev/null 2>&1; echo $?)" -gt 0 ]]; then
echo "Could not find bowtie2-build in your PATH";
exit 127
fi
echo "# "$(date +"%Y-%m-%d %T") bowtie2-build $Bowtie2Build_ExtraParams "$referenceFilePath" "$referenceBasePath"
echo "# "$(bowtie2-build --version | grep -i -E "bowtie.*version")
bowtie2-build $Bowtie2Build_ExtraParams "$referenceFilePath" "$referenceBasePath"
Expand All @@ -144,6 +148,10 @@ elif [[ "$SnpPipeline_Aligner" == "smalt" ]]; then
if [[ $opt_f_set != "1" && -s "$referenceBasePath.smi" && "$referenceBasePath.smi" -nt "$referenceFilePath" ]]; then
echo "# Smalt index $referenceBasePath.smi is already freshly built. Use the -f option to force a rebuild."
else
if [[ "$(which smalt >/dev/null 2>&1; echo $?)" -gt 0 ]]; then
echo "Could not find smalt in your PATH";
exit 127
fi
echo "# "$(date +"%Y-%m-%d %T") smalt index $SmaltIndex_ExtraParams "$referenceBasePath" "$referenceFilePath"
echo "# Smalt "$(smalt version | grep -i -E "Version")
smalt index $SmaltIndex_ExtraParams "$referenceBasePath" "$referenceFilePath"
Expand All @@ -158,6 +166,10 @@ fi
if [[ "$opt_f_set" != "1" && -s "$referenceFilePath.fai" && "$referenceFilePath.fai" -nt "$referenceFilePath" ]]; then
echo "# SAMtools fai index $referenceFilePath.fai is already freshly built. Use the -f option to force a rebuild."
else
if [[ "$(which samtools >/dev/null 2>&1; echo $?)" -gt 0 ]]; then
echo "Could not find samtools in your path"
exit 127
fi
echo "# "$(date +"%Y-%m-%d %T") samtools faidx $SamtoolsFaidx_ExtraParams "$referenceFilePath"
echo "# SAMtools "$(samtools 2>&1 > /dev/null | grep Version)
samtools faidx $SamtoolsFaidx_ExtraParams "$referenceFilePath"
Expand Down