PolITiGenomics

Illumina cluster needs

Thursday, June 18th, 2009 Posted in genomics, IT | No Comments »

There is an interesting thread over at the Solexa Google Group about the IT infrastructure needed to support an Illumina Genome Analyzer (GA). The discussion focuses mostly on the cluster ... Read more..

The ls in lsgmake-gap

Friday, April 3rd, 2009 Posted in genomics, IT | No Comments »

I have released a new version of lsgmake-gap, 0.13 (md5). This version puts the "ls" back in lsgmake-gap by adding the --bsub-options command-line option which allows the user to specify ... Read more..

lsgmake-gap for GAPipeline-1.3

Wednesday, February 25th, 2009 Posted in genomics, IT | 2 Comments »

I have just posted the latest version of lsgmake-gap, 0.12 (md5). This version of lsgmake-gap supports the additional Bustard targets introduced in GAPipeline-1.3 (it should still work with earlier versions ... Read more..

lsgmake-gap-0.9 released

Friday, September 19th, 2008 Posted in genomics, IT | No Comments »

About a year ago Tim Cutts from Sanger suggested I modify (he was being nice, improve is more accurate) lsgmake-gap to use LSF's job arrays rather than spawning a separate ... Read more..

Illumina Genome Analyzer Pipeline and LSF

Friday, March 7th, 2008 Posted in IT | No Comments »

Many centers who use Platform LSF to manage their computational cluster have had trouble running the Illumina (Solexa) Genome Analyzer Pipeline (GAPipeline). The GAPipeline is the series of programs, ... Read more..