Bamtools

https://github.com/pezmaster31/bamtools

Automatic Build

Inside ${HOME}/bioit/apps/bamtools/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/bamtools/SPEC/build 2.5.3

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

module avail bamtools

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

module load bamtools/2.5.3
which bamtools
bamtools --version

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

Manual Build

Download the tar.gz version to be built into /opt/bioit/bamtools/src and untar.

Inside the resulting directory run the following:

mkdir build
cd build
cmake3 -DCMAKE_INSTALL_PREFIX:PATH=/opt/bioit/bamtools/2.5.3 ..
make all
make install

Go into the installation directory (/opt/bioit/bamtools/2.5.3) and copy the launcher from ${HOME}/bioit/apps/bamtools/SPEC/bamtools into it (not into the bin directory. This will sort out the location and execute bamtools with the usual options.

cp ${HOME}/bioit/apps/bamtools/SPEC/bamtools /opt/bioit/bamtools/2.5.3/

Module setup

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

#%Module 1.0
#
#  bamtools module for use with 'environment-modules' package:
#
prepend-path  PATH              /opt/bioit/bamtools/2.5.3

RPM

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

rpmbuild -bb bamtools.spec

This will create an RPM file which you can find in ${HOME}/rpmbuild/RPMS/x86_64. It checks that the installation directory exists and will fail if it isn’t there.

Before you install this, you need to sign it using:

rpm --addsign \
${HOME}/rpmbuild/RPMS/x86_64/bamtools-2.5.3-1.el7.bioit.x86_64.rpm

Now you can move it to /opt/bioit/repo/RPMS

mv ${HOME}/rpmbuild/RPMS/x86_64/bamtools-2.5.3-1.el7.bioit.x86_64.rpm \
/opt/bioit/repo/RPMS

Lastly, run the buildrepo command:

buildrepo

When this finishes, as root you can do the following:

yum clean all
yum update bamtools

That should install the new RPM. If that has worked you can now run the following without loading the module:

bamtools --version

and it should report the correct version. You’re done.