[GenoMax]

OK, I have distmake set up and have a job running on 3 nodes (x 8 = 24 cores).

I am excited.

At the same time, I'm a bit panicked-- as I am worried how or if distmake is supported moving forward? I love , LOVE open source solutions, but I feel a bit more comfortable if the code is in someone's loving hands keeping current.........

Hope the update on distmake is positive

We went from using distmake with SGE to LSF since the lsmake utility in LSF requires a separate license

We are going to continue having this dilemma with software provided by vendors. On one hand I can understand that Illumina is unable to support the multitude of OS configurations at each institution but on the other hand people like us have to make the software work in our environments, no matter what.

You are not alone in this so rest assured that when the next major change from Illumina comes down the pipe, many of us will be attacking that collectively to find a workable solution.

[caseybea]

Yep, it works

OK, well I am thrilled... ECSTATIC ... to report that distmake, hooked into SGE worked flawlessly. The alignment completed like it should.

If you look into the makefiles that ship with CASAVA, I am reasonably sure that there is an issue with PairAux1.mk and PairAux.mk (look at the comments in those files, you'll see what I am referring to).

Sadly, I'm not a programmer and don't posess the knowledge to fix these. It would be awesome if someone else here knew how to address it :-)

Basically, what's going on is some sort of (for lack of a better description), "dependancy leak" that is not an issue with make or distmake, but IS an issue with qmake. (and, I tried multiple flavors of grid engine, all the same issue)

The rub is, Illumina doesn't realize nor admit this, so we're stuck with crappy code. For some reason, it works in THEIR environment. I can't explain why. There are tons of variables between how the data is sequenced, what options are used in the casava alignment step, the coverage of the data, etc etc etc.

As a side note, I found it interesting to learn they do most of their in-house alignments BY LANE (and not flowcell), submitting simple "make -j 4" jobs to their grid (and thus, AVOIDING QMAKE).

The gotcha for us at the moment is, on top of everything else, we're a CAP/CLIA certified clinical lab, and as such, we NEED to use casava because it's all that's clinically licensed so far. Maybe some day someone can figure out how to get other tool(s) like bwa certified. Until then,.....

Anyway, distmake works. I think I only need it for the alignment step, we never had issues with other casava tasks in SGE.