Cutadapt

https://github.com/marcelm/cutadapt

Automatic Build

Inside ${HOME}/bioit/apps/cutadapt/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/cutadapt/SPEC/cutadapt 5.1

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

module avail cutadapt

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

module load cutadapt/5.1
which cutadapt
cutadapt --version

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

Manual Build

Make the directory for the install

mkdir /opt/bioit/cutadapt/5.1

Create a virtual environment for Python3.9

python3.9 -m venv /opt/bioit/cutadapt/5.1/venv

Install cutadapt using pip3

/opt/bioit/cutadapt/5.1/venv/bin/pip3 install --install-option="--install-scripts=/opt/bioit/cutadapt/5.1" cutadapt==5.1

That should be it.

Module setup

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

#%Module 1.0
#
#  cutadapt module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/cutadapt/5.1

RPM

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

rpmbuild -bb cutadapt.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.