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picard-software [2015/03/16 09:01]
aorth [Usage] 		picard-software [2017/12/26 09:55] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 1.129+  * Version: 2.17.0
   * Added: March, 2015   * Added: March, 2015
 +  * Updated: December, 2017
   * Link: https://broadinstitute.github.io/picard   * Link: https://broadinstitute.github.io/picard
  
 ===== 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>
  
-=== Load and run picard === +Load and run picard: 
-<code>$ module load picard/1.129+<code>$ module load picard/2.17.0
 $ picard</code> $ picard</code>
  
 **Note:** Picard tools are CPU hungry; please use a minimum of 6 CPUs in your batch job when running tools from this suite. **Note:** Picard tools are CPU hungry; please use a minimum of 6 CPUs in your batch job when running tools from this suite.
 +
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ cd /tmp +<code>$ sudo mkdir -p /export/apps/picard/2.17.0 
-$ https://github.com/broadinstitute/picard/releases/download/1.129/picard-tools-1.129.zip +$ wget https://github.com/broadinstitute/picard/releases/download/2.17.0/picard.jar 
-$ unzip picard-tools-1.129.zip +$ sudo cp picard.jar /export/apps/picard/2.17.0</code> 
-$ cd picard-tools-1.129 + 
-$ sudo mkdir -p /export/apps/picard/1.129 +I created a generic ''picard'' wrapper for picard tools, as it must otherwise be run with ''java -jar ..'' and is rather user-unfriendly. 
-$ sudo cp -rv * /export/apps/picard/1.129</code>+ 
 +///export/apps/picard/2.17.0/picard//: 
 + 
 +<code>#!/usr/bin/env bash 
 + 
 +readonly PREFIX=$(dirname $0)
  
-I created a generic ''picard'' wrapper for picard tools, as it must otherwise be run with ''java -jar ..'' and is rather unfriendly.+java -jar $PREFIX/picard.jar $*</code>
picard-software.1426496507.txt.gz · Last modified: 2015/03/16 09:01 by aorth

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