Where resource requests are defined

This page documents where resource requests (cpus, mem, tmp space) are defined for major compute steps?

For example:

• BWA alignments in the reference-alignment pipeline: Genome/InstrumentData/AlignmentResult/Bwa.pm
• TopHat alignments in the rna-seq pipeline: Genome/InstrumentData/Command/AlignReads/PerLaneTophat.pm
• Cufflinks in the rna-seq pipeline:
• Cuffdiff in the differential-expression pipeline:

For now these resource requests must be adjusted by modifying the gms-core (aka genome) code directly, however, we are working towards defining some global environment variables that would allow the user to adjust these.