Velvet

VELVET has been deleted so the URL doesn’t work any more.

https://www.ebi.ac.uk/~zerbino/velvet/

Automatic Build

Inside ${HOME}/bioit/apps/velvet/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/velvet/SPEC/build 1.2.10

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

module avail velvet

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

module load velvet/1.2.10
which velvetg
velvetg

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

Manual Build

Download the version to be built into /opt/bioit/velvet/src and untar and cd into the resulting directory. Then run the following:

# Tweak makefile
sed 's+CATEGORIES=2+CATEGORIES=99+g' --in-place Makefile
sed 's+MAXKMERLENGTH=31+MAXKMERLENGTH=255+g' --in-place Makefile
# Compile
make 'OPENMP=8'
# Fix perl shebangs
find . -type f -name '*.pl' | xargs sed 's=/usr/local/bin/perl=/usr/bin/perl=g' --in-place
mkdir /opt/bioit/velvet/1.2.10
mv velveth /opt/bioit/velvet/1.2.10
mv velvetg /opt/bioit/velvet/1.2.10
mv contrib /opt/bioit/velvet/1.2.10

Module setup

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

#%Module 1.0
#
#  velvet module for use with 'environment-modules' package:
#
prepend-path  PATH         /opt/bioit/velvet/1.2.10

RPM

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

rpmbuild -bb velvet.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.