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BauerLab
Analysis Framework for Biological Data from High Throughput Experiments
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A changed tophat/runnow.tmp has no influence on the downstream stages (i.e. cufflinks, htseqcount, bamann). currently all runnow.tmps need to be edited when RUNTOPHATCUFFHTSEQ is run in keep+armed mode A better...
enhancement
Bpipe has a nice representation of the resources consumed in every stage [Bpipe report]("http://code.google.com/p/bpipe/wiki/Reports") 
enhancement