A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
See versions which are available:
$ module avail picard
Run picard (not necessary to load the module file):
$ java -jar /export/apps/picard/2.27.5/picard.jar
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.
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/broadinstitute/picard/releases/download/2.27.5/picard.jar $ sudo mkdir -p /export/apps/picard/2.27.5 $ sudo cp picard.jar /export/apps/picard/2.27.5