Vcftools

https://vcftools.github.io

Automatic Build

Inside ${HOME}/bioit/apps/vcftools/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/vcftools/SPEC/build 0.1.16

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

module avail vcftools

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

module load vcftools/0.1.16
which vcftools
vcftools --version

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

Manual Build

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

./configure --prefix=/opt/bioit/vcftools/0.1.16
make
make install

All perl scripts need to have the following change so that they’ll find the perl modules they need to load:

cd /opt/bioit/vcftools/0.1.16/bin
sed "s+use strict;+use lib '/opt/bioit/vcftools/0.1.16/share/perl5'; use strict;+" \
--in-place *

Module setup

Add a module file in /opt/bioit/modulefiles/vcftools/ 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/vcftools/0.1.16/bin
prepend-path  MANPATH      /opt/bioit/vcftools/0.1.16/share/man

RPM

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

rpmbuild -bb vcftools.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.