Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Picard¶

A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java libraryHTSJDK, supporting accessing of common file formats, such as SAM and VCF, used for high-throughput sequencing data.

Interactive Usage¶

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx or qrsh command, preferably requesting at least 8 Gigabytes of memory

qrsh -l rmem=8G

The latest version of Picard (currently 1.129) is made available with the command

module load apps/binapps/picard

Alternatively, you can load a specific version with

module load apps/binapps/picard/1.129
module load apps/binapps/picard/1.101

These module commands also changes the environment to use Java 1.6 since this is required by Picard 1.129. An environment variable called PICARDHOME is created by the module command that contains the path to the requested version of Picard.

Thus, you can run the program with the command

java -jar $PICARDHOME/picard.jar

Installation notes¶

Version 1.129

A binary install was used. The binary came from the releases page of the project’s github repo

unzip picard-tools-1.129.zip
mkdir -p /usr/local/packages6/apps/binapps/picard
mv ./picard-tools-1.129 /usr/local/packages6/apps/binapps/picard/1.129

Version 1.101

A binary install was used. The binary came from the project’s sourceforge site https://sourceforge.net/projects/picard/files/picard-tools/

unzip picard-tools-1.101.zip
mv ./picard-tools-1.101 /usr/local/packages6/apps/binapps/picard/1.101/

Modulefile¶

Version 1.129

The module file is on the system at /usr/local/modulefiles/apps/binapps/picard/1.129

Its contents are

#%Module1.0#####################################################################
##
## Picard 1.129 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

#This version of Picard needs Java 1.6
module load apps/java/1.6

proc ModulesHelp { } {
        puts stderr "Makes Picard 1.129 available"
}


set version 1.129
set PICARD_DIR /usr/local/packages6/apps/binapps/picard/$version

module-whatis   "Makes Picard 1.129 available"

prepend-path PICARDHOME $PICARD_DIR

Version 1.101

The module file is on the system at /usr/local/modulefiles/apps/binapps/picard/1.101

Its contents are

#%Module1.0#####################################################################
##
## Picard 1.101 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

#This version of Picard needs Java 1.6
module load apps/java/1.6

proc ModulesHelp { } {
        puts stderr "Makes Picard 1.101 available"
}


set version 1.101
set PICARD_DIR /usr/local/packages6/apps/binapps/picard/$version

module-whatis   "Makes Picard 1.101 available"

prepend-path PICARDHOME $PICARD_DIR