Bowtie2

https://github.com/BenLangmead/bowtie2

Automatic Build

Inside ${HOME}/bioit/apps/bowtie2/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/bowtie2/SPEC/build 2.5.4

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

module avail bowtie2

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

module load bowtie2/2.5.4
which bowtie2
bowtie2 --version

Manual Build

Download the src.zip file into /opt/bioit/bowtie2/src and unzip it.

Edit the Makefile to change the value of prefix as follows (change the version as required):

prefix = /opt/bioit/bowtie2/2.5.4

Compile it with the following commands:

make NO_TBB=1
make install

Module setup

Add a module file in /opt/bioit/modulefiles/bowtie2/ for this version by copying previous ones and modifying the paths.

#%Module 1.0
#
#  bowtie2 module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/bowtie2/2.5.4/bin

RPM

There’s a SPEC file for this package in ${HOME}/bioit/apps/bowtie2/SPEC so modify that with the new version details. Once changed, build it with the following command:

rpmbuild -bb bowtie2.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.