Bismark

https://github.com/FelixKrueger/Bismark

Automatic Build

Inside ${HOME}/bioit/apps/bismark/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/bismark/SPEC/build 0.24.2

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

module avail bismark

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

module load bismark/0.24.2
which bismark
bismark --version

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

Manual Build

Note: This is no longer current due to the switch over to using singularity container. See the build script for how that works.

Download the source tarball from here into /opt/bioit/bismark/src, untar it and move it into place as there’s nothing to compile:

mv Bismark-0.24.2 /opt/bioit/bismark/0.24.2

That should be it.

Module setup

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

#%Module 1.0
#
#  bismark module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/bismark/0.24.2/

RPM

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

rpmbuild -bb bismark.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.