Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
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.
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 $PICARDHOME/picard.jar
Version 1.129
A binary install was used. The binary came from the releases page of the project’s github repo
unzip picard-tools-1.129.zip
mkdir -p /usr/local/packages6/apps/binapps/picard
mv ./picard-tools-1.129 /usr/local/packages6/apps/binapps/picard/1.129
Version 1.101
A binary install was used. The binary came from the project’s sourceforge site https://sourceforge.net/projects/picard/files/picard-tools/
unzip picard-tools-1.101.zip
mv ./picard-tools-1.101 /usr/local/packages6/apps/binapps/picard/1.101/
Version 1.129
The module file is on the system at /usr/local/modulefiles/apps/binapps/picard/1.129
Its contents are
#%Module1.0#####################################################################
##
## Picard 1.129 modulefile
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
#This version of Picard needs Java 1.6
module load apps/java/1.6
proc ModulesHelp { } {
puts stderr "Makes Picard 1.129 available"
}
set version 1.129
set PICARD_DIR /usr/local/packages6/apps/binapps/picard/$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