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PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
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Add support for PBS Pro queuing software via shorter job names. #289

Open mseetin opened 8 years ago

mseetin commented 8 years ago

PBS Pro functions a lot like Torque, but for some unknown reason, it has a maximum length for the job name (-N) of 15 characters. This is incompatible with Falcon's lengthy, but human-readable and unique job names that are generated on the fly. This can be addressed with a SHA1 hash of Falcon's job name immediately prior to job submission, keeping only the first 15 hex characters.

While I had thought about accomplishing this via a flexible maximum job name length variable in the config file, it looks like that given how the code currently is, the more elegant solution by far is to add PBSPRO as a job_type option that otherwise leverages the Torque infrastructure and adds the job name hash. This cannot guarantee unique job names, but at 16^15 ~ 10^18 unique hashes, it should be good enough.

pb-cdunn commented 8 years ago

You can do what you want for now. Later, we'll copy/paste your code into the new process-manager, to be released as part of FALCON within about 2 weeks.