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--- picard-software [2015/03/16 09:00] – created aorth
+++ picard-software [2021/05/20 09:14] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.129
+  * Version: 2.17.0
   * Added: March, 2015
+  * Updated: December, 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/2.17.0
 $ 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.
+**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 ======
 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)
+java -jar $PREFIX/picard.jar $*</code>