Bwa
Automatic Build
Inside ${HOME}/bioit/apps/bwa/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/bwa/SPEC/build 0.7.17
When that completes check that the new version is available using:
module avail bwa
If that shows as being there you can test it works with:
module load bwa/0.7.17
which bwa
bwa
Manual Build
Download the tar.bz2 file into /opt/bioit/bwa/src and untar it and go into it.
The Makefile is pretty basic so just type make
When that completes you need to do the following:
mkdir -p ../../0.7.17/bin
mkdir -p ../../0.7.17/man/man1
mv bwa ../../0.7.17/bin/
mv *.pl ../../0.7.17/bin
mv bwa.1 ../../0.7.17/man/man1/
Module setup
Add a module file in /opt/bioit/modulefiles/bwa/ for this version by copying previous ones and modifying the paths.
#%Module 1.0
#
# bwa module for use with 'environment-modules' package:
#
prepend-path PATH /opt/bioit/bwa/0.7.17/bin
prepend-path MANPATH /opt/bioit/bwa/0.7.17/man
RPM
There’s a SPEC file for this package in ${HOME}/bioit/apps/bwa/SPEC so modify that with the new version details. Once changed, build it with the following command:
rpmbuild -bb bwa.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.