stringtie

https://ccb.jhu.edu/software/stringtie/

Automatic Build

Inside ${HOME}/bioit/apps/stringtie/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/stringtie/SPEC/build 3.0.1

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

module avail stringtie

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

module load stringtie/3.0.1
which stringtie
stringtie --version

Manual Build

Download the stringtie-3.0.1.tar.gz file into /opt/bioit/stringtie/src and untar it. Then run the following:

cd stringtie-3.0.1
make release
mkdir /opt/bioit/stringtie/3.0.1
mv stringtie /opt/bioit/stringtie/3.0.1

Module setup

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

#%Module 1.0
#
#  stringtie module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/stringtie/3.0.1

RPM

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

rpmbuild -bb stringtie.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.