This page was last updated on Friday, 11-Nov-2016 09:52:47 CST

Installation notes for Picard version 2.7.1

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Prerequisites

java

Installation version 2.x

1. $ ver="2.7.1"
2. $ cd /usr/local/bin/
3. $ wget -N https://github.com/broadinstitute/picard/releases/download/$ver/picard.jar
4. Make a version-independent symlink. If upgrading, delete the old one first
   
5. Make a wrapper program
   $ nano /usr/local/bin/picard

   #!/bin/bash
   # memory for Java in gigabytes
   defaultjmem=8
   jmem=$defaultjmem
   if [[ $1 =~ ^[0-9]+$ ]] ; then
     jmem=$1
     shift
     echo "Will allocate $jmem gigabytes of memory for Picard"
   fi
   if [[ "$1" == "" ]]; then
     echo "This is a Java wrapper for Picard programs"
     echo "Pass in the name of the picard program to run, followed by any parameters"
     echo "e.g. picard BamIndexStats INPUT=bogus.bam"
     echo "Default memory allocation is $defaultjmem gigabytes"
     echo "To specify an alternate amount, e.g. 16 gigabytes, pass in \"16\" before any other parameters"
     echo "e.g. picard 16 BamIndexStats INPUT=bogus.bam"
     exit 1
   else
     program=$1
     shift
     java -Xmx${jmem}g -jar /usr/local/bin/picard.jar $program $@
     r=$?; if [ $r != 0 ]; then echo "Picard returned error code $r"; fi
     exit $r
   fi

Installation version 1.x

1. $ ver="1.127"
2. $ cd /programinstallers/
3. $ wget -N https://github.com/broadinstitute/picard/releases/download/$ver/picard-tools-$ver.zip
4. $ cd /usr/local/bin
5. $ unzip /programinstallers/picard-tools-$ver.zip
   If upgrading, will replace one file
   ...
     inflating: picard-tools-1.92/snappy-java-1.0.3-rc3.jar
     inflating: picard-tools-1.92/tribble-1.92.jar
     inflating: picard-tools-1.92/variant-1.92.jar
   replace snappy-java-1.0.3-rc3.jar? [y]es, [n]o, [A]ll, [N]one, [r]ename: y
     inflating: snappy-java-1.0.3-rc3.jar
6. Make a version-independent symlink. If upgrading, delete the old one first
   $ rm picard-tools
7. $ ln -s picard-tools-$ver picard-tools
8. Make a wrapper program
   $ nano /usr/local/bin/picard

   #!/bin/bash
   # memory for Java in gigabytes
   defaultjmem=8
   jmem=$defaultjmem
   if [[ $1 =~ ^[0-9]+$ ]] ; then
     jmem=$1
     shift
     echo "Will allocate $jmem gigabytes of memory for Picard"
   fi
   if [[ "$1" == "" ]]; then
     echo "This is a Java wrapper for Picard programs"
     echo "Pass in the name of the picard program to run, followed by any parameters"
     echo "e.g. picard BamIndexStats INPUT=bogus.bam"
     echo "Default memory allocation is $defaultjmem gigabytes"
     echo "To specify an alternate amount, e.g. 16 gigabytes, pass in \"16\" before any other parameters"
     echo "e.g. picard 16 BamIndexStats INPUT=bogus.bam"
     exit 1
   else
     program=$1
     shift
     java -Xmx${jmem}g -jar /usr/local/bin/picard-tools/picard.jar $program $@
     r=$?; if [ $r != 0 ]; then echo "Picard returned error code $r"; fi
     exit $r
   fi