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Update run.py to support Torque qsub#227
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pb-cdunn merged 1 commit intoPacificBiosciences:masterfrom Oct 19, 2015
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Added support for PBS torque job_type = "torque" can now be used in the CFG file Here is an example of what to place in the CFG file job_type = torque sge_option_da = -l nodes=1:ppn=16:compute,walltime=4:00:00 sge_option_la = -l nodes=1:ppn=16:compute,walltime=4:00:00 sge_option_pda = -l nodes=1:ppn=16:compute,walltime=4:00:00 sge_option_pla = -l nodes=1:ppn=16:compute,walltime=4:00:00 sge_option_fc = -l nodes=1:ppn=16:compute,walltime=4:00:00 sge_option_cns = -l nodes=1:ppn=16:compute,walltime=4:00:00
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We definitely want torque support, but the new code looks almost the same as sge. It has |
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Yes, it is the correct option parameter for -j on systems with torque. |
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Ok. I couldn't find anything on For reference: Common commands in TORQUE and SGE. |
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Added to FAQ. |
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I worked it out with our HPC guys and have it working with torque |
pb-cdunn
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Oct 19, 2015
Update run.py to support Torque qsub
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Sorry. Somehow I had accidentally closed instead of merging. |
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Apr 18, 2019
…-erc_from_daligner to develop * commit 'e48b9efebbcb254d83341fd21a6d6280fb482dd6': The falcon_kit.mains.consensus can now accept externally provided mapping coordinates together with the sequences. If provided, and if an optional argument --allow-external-mapping is specified, the error correction code will not map internally. - Refactoring of the code duplication in get_consensus_with_trim and get_consensus_without_trim. - Added a SeqTuple named tuple in the consensus.py, to allow simpler passing of additional arguments. - Updated the falcon_kit/mains/consensus.py to be able to output the alignment ranges provided by DALIGNER all the way to the consensus .c code. - The new feature of using external coordinates is a no-op unless --allow-external-mapping is specified. This is intentionally done to feature flag it. The error correction stage can now accept external mapping coordinates. - Implemented the generate_consensus_from_mapping which uses the mapping coordinates provided via the parameters. Added log statements around asserts. Added some debug logging too. - Properly handling leading indels in generate_consensus_from_mapping now. The get_cns_from_align_tags method expects the first op to be a match/mismatch, and this causes out of bounds issues when adding edges to the predecessor. - Additionally, range coordinates passed to get_align_tags needed to be updated as well.
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Added support for PBS torque.
job_type = torquecan now be used in the CFG file.Here is an example of what to place in the CFG file