SOAPdenovo2

http://soap.genomics.org.cn/soapdenovo.html

Automatic Build

Inside ${HOME}/bioit/apps/SOAPdenovo2/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/SOAPdenovo2/SPEC/build 242

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

module avail SOAPdenovo2

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

module load SOAPdenovo2/242
which SOAPdenovo-63mer
SOAPdenovo-63mer --version

Note this reports a different version (2.04 in this case) but that’s expected.

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

Manual Build

Download the tar.gz file into /opt/bioit/SOAPdenovo2/src and untar it.

Build is simple, just make and then mv the resulting SOAPdenovo-* binaries into place:

make
mkdir /opt/bioit/SOAPdenovo2/242/
mv SOAPdenovo-* /opt/bioit/SOAPdenovo2/242/

Module setup

Add a module file in /opt/bioit/modulefiles/SOAPdenovo2/ for this version by copying previous ones and modifying the paths.

#%Module 1.0
#
#  SOAPdenovo2 module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/SOAPdenovo2/242

RPM

There’s a SPEC file for this package in ${HOME}/bioit/apps/SOAPdenovo2/SPEC so modify that with the new version details. Once changed, build it with the following command:

rpmbuild -bb SOAPdenovo2.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.