IGV

https://github.com/igvteam/igv

Automatic Build

Inside ${HOME}/bioit/apps/igv/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/igv/SPEC/build 2.19.4

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

module avail igv

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

module load igv/2.19.4
which igv

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

Manual Install

Get the Linux zip file from https://software.broadinstitute.org/software/igv/download and unzip it in the src directory. Then you just need to move the unzipped directory into its final location:

mv IGV_Linux_2.19.4 /opt/bioit/igv/2.19.4

Rename the run script:

mv /opt/bioit/igv/2.19.4/igv.sh /opt/bioit/igv/2.19.4/igv

That should be enough for users to launch this version.

Module setup

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

#%Module 1.0
#
#  igv module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/igv/2.19.4/

RPM

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

cp ${HOME}/bioit/apps/igv/SPEC/igv.desktop ${HOME}/rpmbuild/SOURCES
cp ${HOME}/bioit/apps/igv/SPEC/igv-icons.tar.gz ${HOME}/rpmbuild/SOURCES
cp ${HOME}/bioit/apps/igv/SPEC/bioinformatics* ${HOME}/rpmbuild/SOURCES
rpmbuild -bb igv.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.