Gvcftools

https://github.com/sequencing/gvcftools

Automatic Build

Inside ${HOME}/bioit/apps/gvcftools/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/gvcftools/SPEC/build 0.17.0

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

module avail gvcftools

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

module load gvcftools/0.17.0
which twins
twins --version

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

Manual Build

Download the version to be built into /opt/bioit/gvcftools/src and untar

make
mkdir /opt/bioit/gvcftools/0.17.0
mv bin /opt/bioit/gvcftools/0.17.0/

Module setup

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

#%Module 1.0
#
#  vcftools module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/gvcftools/0.17.0/bin

RPM

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

rpmbuild -bb gvcftools.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.