BBMap

https://sourceforge.net/projects/bbmap/

Automatic Build

Inside ${HOME}/bioit/apps/bbmap/SPEC there is a script called build. This just requires the version number and will download, compile, install and create the module file for you. Execute it as follows:

${HOME}/bioit/apps/bbmap/SPEC/build 39.28

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

module avail bbmap

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

module load bbmap/39.28
which bbduk.sh
bbduk.sh --version

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

Manual Build

The version_check script will show there’s a new version available but it can’t download it so you’ll need to go to the homepage and get it directly.

Download the version to be built into /opt/bioit/bbmap/src and untar

There’s nothing to actually build so just run the following to move the files and correct the permissions:

mv bbmap ../39.28
chmod 755 ../39.28
cd ../39.28
chmod -R 755 *

Module setup

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

#%Module 1.0
#
#  bbmap module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/bbmap/39.28

RPM

There’s a SPEC file for this package in ${HOME}/bioit/apps/bbmap/SPEC so modify that with the new version details. The /opt/bioit/bbmap/39.28/doc/changelog.txt will give you the details for the %changelog section of the SPEC file.

Once changed, build it with the following command:

rpmbuild -bb bbmap.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 th ere.

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

rpm --addsign \
${HOME}/rpmbuild/RPMS/x86_64/bbmap-39.28-1.el7.bioit.x86_64.rpm

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

mv ${HOME}/rpmbuild/RPMS/x86_64/bbmap-39.28-1.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 bbmap

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

bbduk.sh --version

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