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

• Version: 1.129
• Added: March, 2015
• Link: https://broadinstitute.github.io/picard

$ module avail picard

$ module load picard/1.129
$ 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
$ https://github.com/broadinstitute/picard/releases/download/1.129/picard-tools-1.129.zip
$ unzip picard-tools-1.129.zip
$ cd picard-tools-1.129
$ sudo mkdir -p /export/apps/picard/1.129
$ sudo cp -rv * /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 unfriendly.