From their website; "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom."

Download the (unnumbered, but usefully named) tarball. Untar (tar xvf velvet_latest.tgz) in a sensible place (e.g., /usr/local/src/VELVET). The GPL license and a handy manual is included. Load the necessary module (code>module load gcc) and make a path to a working directory (e.g., mkdir -p /usr/local/velvet/0.7.31).

Discover that the damn thing is preconfigured and and thus requires the source to be copied to the working directory (cp -r /usr/local/src/VELVET/0.7.31 /usr/local/velvet/0.7.31).

Run make. Be surprised by how short it is and how quickly it loads.

Run the necessary tests:


./velveth
./velvetg
./velveth sillyDirectory 21 -shortPaired data/test_reads.fa
./velvetg sillyDirectory
less sillyDirectory/stats.txt
./velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amos_file yes
./velvetg sillyDirectory -exp_cov 19 -ins_length 100
./velveth sillyDirectory 21 -short data/test_reads.fa -long data/test_long.fa
./velvetg sillyDirectory -exp_cov 19


Create module file (mkdir /usr/local/Modules/modulefiles/velvet/, nano /usr/local/Modules/modulefiles/velvet/0.7.31


#%Module1.0#####################################################################
##
## $name modulefile
##
set ver [lrange [split [ module-info name ] / ] 1 1 ]
set name [lrange [split [ module-info name ] / ] 0 0 ]
set subver [lrange [split $ver - ] 0 0 ]
proc ModulesHelp { } {
puts stderr "\tThis module sets the envinronment for $name v$ver"
}
module-whatis "Set environment variables to use $name version $ver"
prepend-path PATH /usr/local/$name/$ver
system /usr/local/recluse/scripts/vpac/test_group_member $name