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--- picard-software [2017/12/26 09:50] – aorth
+++ picard-software [2022/11/21 08:01] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 2.8.2
+  * Version: 2.27.5
   * Added: March, 2015
-  * Updated: February, 2017
+  * Updated: November, 2022
-  * Link: https://broadinstitute.github.io/picard
+  * Link: https://github.com/broadinstitute/picard
 ===== Usage =====
-See versions of picard which are available:
+See versions which are available:
 <code>$ module avail picard</code>
-Load and run picard:
+Run picard (not necessary to load the module file):
-<code>$ module load picard/2.8.2
+<code>$ java -jar /export/apps/picard/2.27.5/picard.jar</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 makes use of temporary storage in ''/tmp'' during analysis by default. You will probably run into "No space left on device" errors unless you specify a different temp directory, for example: ''TMP_DIR=/var/scratch''.
 ===== Installation ======
@@ Line 23: / Line 24: @@
 <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/2.27.5/picard.jar
-$ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/</code>
+$ sudo mkdir -p /export/apps/picard/2.27.5
+$ sudo cp picard.jar /export/apps/picard/2.27.5</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>