Latest PICARD-tools installation (from v1.124)

2014/11/14 20:59:28

PICARD Homepage

http://broadinstitute.github.io/picard/

https://github.com/broadinstitute/picard

Here I am not going to introduce how excellent and useful this toolset is, but to celebrate the the author finally integrate all tools into one package. So you will not need to find the package name every time you want it. Actually it’s boring to do that: set PICARDHOME or PICARD_HOME to the package root directory and find a package you want, and java –jar PACKAGE_NAME [options] ….

Now I am happy to to see all the functions are integrated into one package ‘picard.jar’. so you would just call

$ java –jar PICARDHOME/picard.jar

Here I am giving my way to install PICARDtools and use it simply.

Installation (Linux):

1. create a directory you want to install PICARDtools

$ mkdir -p $HOME/programs/picard/v1.124/x86_64

$ cd $HOME/programs/picard/v1.124/x86_64

2. Download the software from github

$ wget https://github.com/broadinstitute/picard/releases/download/1.124/picard-tools-1.124.zip

$ unzip picard-tools-1.124.zip

$ ls

picard-tools-1.124

$ mv picard-tools-1.124 bin

$ cd bin

$ ls -1

htsjdk-1.124.jar

libIntelDeflater.so

picard.jar

picard-lib.jar

3. [optional] create one link to directly call picard.jar

$ vim picard

#press i on your keyboard to enter VIM edit mode

#pasta following into terminal:

-——————————file border—do not copy this line——————————-

#!/bin/sh

CurDir=$(cd `dirname $(readlink -f $0)`; pwd)

java -jar $CurDir/picard.jar "$@"

-—————————–file border—–do not copy this line—————————–

#press Esc, and then input :wq to save and exit

#This is to create one file containing content described above. Same with other text editor, like gedit

$ chmod +x ./picard

#And then put this picard file into you PATH by editing ~/.bashrc, /etc/profile or other ways.

$ export PATH=$HOME/programs/picard/v1.124/x86_64/bin:$PATH

in my case, to make the setting immediately work. But remember to change the picardpath to yours.

4. test

$ picard

PicardCommandLine [-h]

…..

#To use subfunctions: just call that behind picard, like:

$ picard SamToFastq

#To see options help of SamToFastq

……