lsgmake-gap for GAPipeline-1.3
February 25th, 2009
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 of GAPipeline). It also adds support for auto-calibration in GERALD (QCAL_SOURCE autoN). The script automatically detects whether auto-calibration was requested by scanning the GERALD configuration file and submits the appropriate jobs. Finally, I also put in a workaround for a GNU make bug we were hitting when running “make -j N all” with N > 1 after an unsuccessful attempt had already been made to build the “all” target (make would get confused and max out the CPU in an infinite loop). The fix, simply, was to run every “all” target without parallel jobs. Unlike previous versions of GAPipeline, 1.3 does very little in the all target, so this has negligible effect on performance. This version has been extensively tested in our environment so you should not run into any problems upgrading.
Posted in IT, genomics | 2 Comments »
Tagged with: genomics, Illumina, IT, LSF, wustl
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February 25th, 2009 at 7:59 pm
Negligible effect, not affect.
February 25th, 2009 at 9:58 pm
Corrected.