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--- picard-software [2015/03/16 09:00] – created aorth
+++ picard-software [2017/02/06 07:50] – old revision restored (2017/02/05 16:18) joguya
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.129
+  * Version: 2.8.2
   * Added: March, 2015
+  * Updated: February, 2017
   * Link: https://broadinstitute.github.io/picard
 ===== Usage =====
-=== See versions of picard which are available ===
+See versions of picard which are available:
 <code>$ module avail picard</code>
-=== Load and run picard ===
+Load and run picard:
-<code>$ module load picard/1.129
+<code>$ module load picard/2.8.2
 $ 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 ======
@@ Line 23: / Line 24: @@
 <code>$ cd /tmp
-$ https://github.com/broadinstitute/picard/releases/download/1.129/picard-tools-1.129.zip
+$ wget https://github.com/broadinstitute/picard/releases/download/2.8.2/picard-2.8.2.jar
-$ unzip picard-tools-1.129.zip
+$ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/
-$ cd picard-tools-1.129
+</code>
-$ sudo mkdir -p /export/apps/picard/1.129
-$ sudo cp -rv * /export/apps/picard/1.129</code>
+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/picard/2.8.2/picard<code>#!/usr/bin/env bash
+readonly PREFIX=$(dirname $0)
+java -jar $PREFIX/picard.jar $*
+</code>