krishna: clean up seqer and matrix code
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This involves putting seqer and matrix in their own cmd directories and possibly generating or otherwise the options in matrix.
@kortschak Please add executable of krishna-matrix, gffer and seqer. Can we also change the default malloc.go running time to 40 to handle big jobs?
/cc @dadelson
Can we also change the default malloc.go running time to 40 to handle big jobs?
No, this is not in our hands.
The original problem with the matrix program was that it needed to be altered for each krishna job set. What I will do is get matrix to take a string parameter called krishnaflags that is organised appropriately to send to krishna.
Yeah, you right! That's what we just talked about, please do that, so we don't need to build every time after change krishna parameters.