We recently ported Velvet, a short sequence assembler, to our cluster. It can be compiled with multi-threading via OMP, however there does not seem to be an elegant way to control its behaviour in a clustered environment other than to use PBS directives to book an entire node. The problem here is that a user would need a completely free node to start with. We'll see how well this works, however we may elect to recompile the application without OMP support.
In addition to Velvet we installed the Velvet Optimiser. This is very simple to install, however one of the requirements is apparently BioPerl. This install was a bit more complex and required an install base directive to ensure that the scripts ended up in the NFS application mount.
Velvet is memory hungry, on a node with 4GB of RAM an assembly took over an hour to reconstruct, whereas on a node with 24GB or RAM the same read took just over a minute. We're hoping that this application is swiftly ported to Grid format as our site has a distinct lack of large memory machines.
