A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
See versions of picard which are available:
$ module avail picard
Load and run picard:
$ module load picard/2.8.2 $ 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/2.8.2/picard-2.8.2.jar $ sudo cp picard-2.8.2.jar /export/apps/picard/2.8.2/
I created a generic
picard wrapper for picard tools, as it must otherwise be run with
java -jar .. and is rather user-unfriendly.
#!/usr/bin/env bash readonly PREFIX=$(dirname $0) java -jar $PREFIX/picard.jar $*