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picard-software [2017/02/06 07:49] – [Installation] joguyapicard-software [2017/12/26 09:50] – aorth
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 ===== Usage ===== ===== Usage =====
- 
 See versions of picard which are available: See versions of picard which are available:
 <code>$ module avail picard</code> <code>$ module avail picard</code>
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 <code>$ cd /tmp <code>$ cd /tmp
 $ wget https://github.com/broadinstitute/picard/releases/download/2.8.2/picard-2.8.2.jar $ wget https://github.com/broadinstitute/picard/releases/download/2.8.2/picard-2.8.2.jar
-$ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/ +$ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/</code>
-</code>+
  
-I created a generic ''GenomeAnalysisTK'' wrapper shell script for GATK, as it must otherwise be run with ''java -jar ..'' and is rather user-unfriendly.+I created a generic ''picard'' wrapper for picard tools, as it must otherwise be run with ''java -jar ..'' and is rather user-unfriendly.
  
-/export/apps/gatk/3.7.0/GenomeAnalysisTK.jar<code>#!/usr/bin/env bash+///export/apps/picard/2.8.2/picard//: 
 + 
 +<code>#!/usr/bin/env bash
  
 readonly PREFIX=$(dirname $0) readonly PREFIX=$(dirname $0)
  
-java -jar $PREFIX/GenomeAnalysisTK.jar $*+java -jar $PREFIX/picard.jar $*
 </code> </code>
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picard-software.txt · Last modified: 2022/11/21 08:01 by aorth