Picard

https://github.com/broadinstitute/picard

Automatic Build

Inside ${HOME}/bioit/apps/picard/SPEC there is a script called build. This just requires the version number and will download, compile, install and create the modulefile for you. Execute it as follows:

${HOME}/bioit/apps/picard/SPEC/build 3.4.0

When that completes check that the new version is available using:

module avail picard

If that shows as being there you can test it works with:

module load picard/3.4.0
which picard
picard SortVcf --version

If all is good, you can move to the RPM building step.

Manual Build

From version 3.4.0, picard requires Java 17 so do the following before trying to build picard itself:

cd /opt/bioit
wget https://download.java.net/java/GA/jdk17.0.2/dfd4a8d0985749f896bed50d7138 ee7f/8/GPL/openjdk-17.0.2_linux-x64_bin.tar.gz
tar xvf openjdk-17.0.2_linux-x64_bin.tar.gz
rm openjdk-17.0.2_linux-x64_bin.tar.gz

Once you’ve got Java you need to set these two variables before doing the clone:

export JAVA_HOME=/opt/bioit/jdk-17.0.2
export PATH=$PATH:$JAVA_HOME/bin

Now you have to clone the git repo into /opt/bioit/picard/src using the following:

cd /opt/bioit/picard/src
git clone -b 3.4.0 https://github.com/broadinstitute/picard.git
mv picard picard-3.4.0

Build the picard.jar file by running the following:

cd picard-3.4.0
./gradlew shadowJar

Now make a directory for the jar to go into and move it into there:

mkdir /opt/bioit/picard/3.4.0
mv build/libs/picard.jar /opt/bioit/picard/3.4.0

Finally, copy the picard wrapper from inside the SPEC directory of the git repository:

cp ~/bioit/apps/picard/SPEC/picard /opt/bioit/picard/3.4.0

This wrapper figures out what directory it is in and sets picard_dir to that so there’s no need to edit it.

Now users will just be able to run picard from the command line without all that messing around with calling java -jar.

Module setup

Add a module file in /opt/bioit/modulefiles/picard/ for this version by copying previous ones and modifying the paths.

#%Module 1.0
#
#  picard module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/picard/3.4.0/

RPM

There’s a SPEC file for this package in ${HOME}/bioit/apps/picard/SPEC so modify that with the new version details. Once changed, build it with the following command:

rpmbuild -bb picard.spec

This will create an installable RPM file which you can find in ${HOME}/rpmbuild/RPMS/x86_64 and just install that. It checks that the installation directory exists and will fail if it isn’t there.