TopHat

https://ccb.jhu.edu/software/tophat/index.shtml

Automatic Build

Inside ${HOME}/bioit/apps/tophat/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/tophat/SPEC/build 2.1.1

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

module avail tophat

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

module load tophat/2.1.1
which tophat
tophat --version

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

Manual Build

Download the tar.gz file into /opt/bioit/tophat/src and untar it.

Configure and make with the following:

./configure --prefix=/opt/bioit/tophat/2.1.1
make
make install

Module setup

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

#%Module 1.0
#
#  tophat module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/tophat/2.1.1/bin

RPM

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

rpmbuild -bb tophat.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.