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

===== Information =====

  * Version: 2.17.0
  * Added: March, 2015
  * Updated: December, 2017
  * Link: https://broadinstitute.github.io/picard

===== Usage =====
See versions of picard which are available:
<code>$ module avail picard</code>

Load and run picard:
<code>$ module load picard/2.17.0
$ picard</code>

**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:

<code>$ 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</code>

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//:

<code>#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/picard.jar $*</code>