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picard-software

Picard tools

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

Information

Usage

See versions of picard which are available:

$ module avail picard

Load and run picard:

$ module load picard/2.17.0
$ picard

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

Installation

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/picard/2.17.0
$ wget https://github.com/broadinstitute/picard/releases/download/2.17.0/picard.jar
$ sudo cp picard.jar /export/apps/picard/2.17.0

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

/export/apps/picard/2.17.0/picard:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/picard.jar $*
picard-software.txt · Last modified: 2017/12/26 12:55 by aorth