/usr/bin/picard-tools is in picard-tools 1.113-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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set -eu
if [ `basename -- $0` = picard-tools ]; then
if [ $# = 0 ]; then
cat 1>&2 <<EOF
picard-tools: missing command argument
Try \`picard-tools --help' for more information.
EOF
exit 1
fi
command=`basename -- $1`
shift
else
command=`basename $0`
fi
case $command in
AddOrReplaceReadGroups) main=net.sf.picard.sam.AddOrReplaceReadGroups;;
AddCommentsToBam) main=net.sf.picard.sam.AddCommentsToBam;;
BamIndexStats) main=net.sf.picard.sam.BamIndexStats;;
BamToBfq) main=net.sf.picard.fastq.BamToBfq;;
BuildBamIndex) main=net.sf.picard.sam.BuildBamIndex;;
CalculateHsMetrics) main=net.sf.picard.analysis.directed.CalculateHsMetrics;;
CheckIlluminaDirectory) main=net.sf.picard.illumina.CheckIlluminaDirectory;;
CleanSam) main=net.sf.picard.sam.CleanSam;;
CollectAlignmentSummaryMetrics) main=net.sf.picard.analysis.CollectAlignmentSummaryMetrics;;
CollectGcBiasMetrics) main=net.sf.picard.analysis.CollectGcBiasMetrics;;
CollectInsertSizeMetrics) main=net.sf.picard.analysis.CollectInsertSizeMetrics;;
CollectMultipleMetrics) main=net.sf.picard.analysis.CollectMultipleMetrics;;
CollectRnaSeqMetrics) main=net.sf.picard.analysis.CollectRnaSeqMetrics;;
CollectTargetedPcrMetrics) main=net.sf.picard.analysis.CollectTargetedPcrMetrics;;
CollectWgsMetrics) main=net.sf.picard.analysis.CollectWgsMetrics;;
CompareSAMs) main=net.sf.picard.sam.CompareSAMs;;
CreateSequenceDictionary) main=net.sf.picard.sam.CreateSequenceDictionary;;
DownsampleSam) main=net.sf.picard.sam.DownsampleSam;;
EstimateLibraryComplexity) main=net.sf.picard.sam.EstimateLibraryComplexity;;
ExtractIlluminaBarcodes) main=net.sf.picard.illumina.ExtractIlluminaBarcodes;;
ExtractSequences) main=net.sf.picard.reference.ExtractSequences;;
FastqToSam) main=net.sf.picard.sam.FastqToSam;;
FilterSamReads) main=net.sf.picard.sam.FilterSamReads;;
FixMateInformation) main=net.sf.picard.sam.FixMateInformation;;
IlluminaBasecallsToFastq) main=net.sf.picard.illumina.IlluminaBasecallsToFastq;;
IlluminaBasecallsToSam) main=net.sf.picard.illumina.IlluminaBasecallsToSam;;
IntervalListTools) main=net.sf.picard.util.IntervalList;;
MarkDuplicates) main=net.sf.picard.sam.MarkDuplicates;;
MeanQualityByCycle) main=net.sf.picard.analysis.MeanQualityByCycle;;
MergeBamAlignment) main=net.sf.picard.sam.MergeBamAlignment;;
MergeSamFiles) main=net.sf.picard.sam.MergeSamFiles;;
MergeVcfs) main=net.sf.picard.vcf.MergeVcfs;;
NormalizeFasta) main=net.sf.picard.reference.NormalizeFasta;;
QualityScoreDistribution) main=net.sf.picard.analysis.QualityScoreDistribution;;
ReorderSam) main=net.sf.picard.sam.ReorderSam;;
ReplaceSamHeader) main=net.sf.picard.sam.ReplaceSamHeader;;
RevertSam) main=net.sf.picard.sam.RevertSam;;
SamFormatConverter) main=net.sf.picard.sam.SamFormatConverter;;
SamToFastq) main=net.sf.picard.sam.SamToFastq;;
SortSam) main=net.sf.picard.sam.SortSam;;
SplitVcfs) main=net.sf.picard.vcf.SplitVcfs;;
ValidateSamFile) main=net.sf.picard.sam.ValidateSamFile;;
VcfFormatConverter) main=net.sf.picard.vcf.VcfFormatConverter;;
ViewSam) main=net.sf.picard.sam.ViewSam;;
--help)
cat <<EOF
Usage: picard-tools COMMAND [OPTION]...
See \`man picard-tools' for a list of COMMANDs.
EOF
exit 0;;
--version)
cat <<EOF
picard-tools
Copyright 2010 The Broad Institute
EOF
exit 0;;
*) echo 1>&2 picard-tools: unrecognized command "'$command'"; exit 1
esac
p=/usr/share/java
exec java ${JAVA_OPTIONS-} -XX:MaxPermSize=256m -cp $p/jbzip2.jar:$p/picard.jar:$p/sam.jar:$p/cofoja.jar:$p/commons-jexl2.jar $main "$@"
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