More proteomics software fun.

So we finally have Pecan up and running on Emu! It took some doing however. Here’s a little list of the things I had to do to make it work.

First, Grid Engine. What a pain. It’s very picky about host IP and resolved names matching up. I eventually found a guide for installation and configuring that worked.

Second, Pecan requires pymzml, a python package. However the package version distributed by PIP does not contain the proper psi-ms-4.0.1.obo file in the package for Pecan to run. The file, and associated issue for the pymzml developers can be found here

Then came the pecanpie oddities. Pecanpie is an accessory program that sets up a series of job files for Grid Engine. It adds an argument to each grid engine call-l mem_requested = xxG which I originally thought to be an argument passed on to the Pecan or Percolator programs, but after talking to the
developer of Pecan, this is an argument for Grid Engine itself which, depending on the version, can also be mem_free. There is a space to change this in the config file for Pecan, but that requires a re-compile of pecan to fix.

Emu is currently running full tilt on Laura’s proteomic data, using 14/16 cores at the moment, and every scrap of free memory. Pecan originally wanted 92gb of memory to run, so hopefully it will behave having only half of that. Hyak will definitely be exciting for future proteomics work.