A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.

• Version: 1.133
• Added: March, 2015
• Updated: June, 2015
• Link: https://broadinstitute.github.io/picard

See versions of picard which are available:

$ module avail picard

Load and run picard:

$ module load picard/1.133
$ picard

Note: Picard tools are CPU hungry; please use a minimum of 6 CPUs in your batch job when running tools from this suite.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/broadinstitute/picard/releases/download/1.133/picard-tools-1.133.zip
$ unzip picard-tools-1.133.zip
$ cd picard-tools-1.133
$ sudo mkdir /export/apps/picard/1.133
$ sudo cp -rv * /export/apps/picard/1.133

I created a generic picard wrapper for picard tools, as it must otherwise be run with java -jar .. and is rather unfriendly.

/export/apps/picard/1.133/picard

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/picard.jar $*