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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Allow progressive cactus to use UGE #82

Closed ndukler closed 6 years ago

ndukler commented 6 years ago

The cluster I use has UGE (Univa Grid Engine) on it, not SGE. The jobs are being submitted using options that are not valid on my system: (1) -l num_proc=1.0. If this is the number of threads per job then it should be “-pe threads” instead of “-l num_proc”.

(2) “-l virtual_free” is equivalent to “-l m_mem_free”.

ndukler commented 6 years ago

Figured it out. Made alterations to gridengine.py in the jobTree module. Just had to alter the prepareQsub function.

joelarmstrong commented 6 years ago

Nice. I will make a note in the toil repository so that we can support UGE as well as SGE. (toil is the new version of jobTree, and the next version of Cactus will use toil).

ndukler commented 6 years ago

It might be useful to create a template for people to customize how the flags are constructed since I understand some of them vary from system to system, even within a single type of queue management software. Thanks for making a note!