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benedictpaten / jobTree

Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
MIT License
24 stars 18 forks source link

jobTree support for argparse #6

Closed dentearl closed 12 years ago

dentearl commented 12 years ago

optparse is deprecated, argparse is the replacement. This can be patched by checking the .class of the input in the addOptions() function contained in jobTree.src.jobTreeRun BUT will also need to be changed in sonLib.bioio addLoggingOptions(). I think the way jobTree and sonLib have used optparse is generic enough that the transition would be transparent to script writers.

benedictpaten commented 12 years ago

Be my guest..

On Fri, Nov 2, 2012 at 10:58 AM, Dent Earl notifications@github.com wrote:

optparse http://docs.python.org/2/library/optparse.html is deprecated, argparse http://docs.python.org/2/library/argparse.html#module-argparseis the replacement. This can be patched by checking the .class of the input in the addOptions() function contained in jobTree.src.jobTreeRun BUT will also need to be changed in sonLib.bioio addLoggingOptions(). I think the way jobTree and sonLib have used optparse is generic enough that the transition would be transparent to script writers.

— Reply to this email directly or view it on GitHubhttps://github.com/benedictpaten/jobTree/issues/6.

dentearl commented 12 years ago

Changes applied in jobTree commit 33c4defbbb542183bbf2e60e712c552c770346ce and sonLib commit 995fdccf65cce7180899f2dbe1a966dcb6b2ba13. Closing.