Samtools

http://www.htslib.org/

Automatic Build

Inside ${HOME}/bioit/apps/samtools/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/samtools/SPEC/build 1.22

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

module avail samtools

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

module load samtools/1.22
which samtools
samtools --version

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

Manual Build

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

Inside the source run the following where 1.22 is the current one being built:

./configure --prefix=/opt/bioit/samtools/1.22
make
make install

Module setup

Add a module file in /opt/bioit/modulefiles/samtools/ for this version by copying previous ones and modifying the paths. Note that this file loads bcftools/1.22 as a dependency since samtools and bcftools should be used together.

#%Module 1.0
#
#  samtools module for use with 'environment-modules' package:
#
module load bcftools/1.22
prepend-path  PATH         /opt/bioit/samtools/1.22/bin
prepend-path  MANPATH      /opt/bioit/samtools/1.22/share/man

RPM

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

rpmbuild -bb samtools.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.