FastQC

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Automatic Build

Inside ${HOME}/bioit/apps/FastQC/SPEC there is a script called build. This j ust requires the version number and will download, compile, install and create t he modulefile for you. Execute it as follows:

${HOME}/bioit/apps/FastQC/SPEC/build 0.12.1

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

module avail FastQC

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

module load FastQC/0.12.1
which FastQC

Manual Build

Download the Linux zip version to be built into /opt/bioit/FastQC/src and unzip.

The resulting FastQC directory should be moved to a versioned directory and the fastqc command made executable:

mv FastQC ../0.12.1
cd ../0.12.1
chmod 755 fastqc

Module setup

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

#%Module 1.0
#
#  FastQC module for use with 'environment-modules' package:
#
prepend-path  PATH              /opt/bioit/FastQC/0.12.1

RPM

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

rpmbuild -bb FasqtQC.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.