picard-software
This is an old revision of the document!
Table of Contents
Picard tools
A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
Information
- Version: 1.133
- Added: March, 2015
- Updated: June, 2015
Usage
See versions of picard which are available:
$ module avail picard
Load and run picard:
$ module load picard/1.133 $ 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:
$ cd /tmp $ wget https://github.com/broadinstitute/picard/releases/download/1.133/picard-tools-1.133.zip $ unzip picard-tools-1.133.zip $ cd picard-tools-1.133 $ sudo mkdir /export/apps/picard/1.133 $ sudo cp -rv * /export/apps/picard/1.133
I created a generic picard
wrapper for picard tools, as it must otherwise be run with java -jar ..
and is rather unfriendly.
/export/apps/picard/1.133/picard
#!/usr/bin/env bash readonly PREFIX=$(dirname $0) java -jar $PREFIX/picard.jar $*
picard-software.1433941122.txt.gz · Last modified: 2015/06/10 12:58 by joguya