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SLURM wrapper added for pyani #236

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SLURM wrapper added for pyani #236

wants to merge 13 commits into from

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TSL-RamKrishna
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Two changes I made in pyani

  1. I have added slurm scheduler wrapper for pyani.
  2. When running ANIb and ANIblastall with scheduler, blastn command execution fails. My codes writes the blastn commands to a bash file and executes the file.

@widdowquinn widdowquinn self-assigned this Feb 3, 2021
@widdowquinn widdowquinn added the enhancement something we'd like pyani to do that it doesn't already label Feb 3, 2021
@widdowquinn widdowquinn added this to the 0.3.0 milestone Feb 3, 2021
@widdowquinn widdowquinn linked an issue Feb 3, 2021 that may be closed by this pull request
Add SLURM support #215
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@widdowquinn
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Thanks - one of my routes to testing SLURM is down ATM, but I'll get to this as soon as I can.

@widdowquinn widdowquinn mentioned this pull request Jun 16, 2021
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@widdowquinn
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Many thanks again @TSL-RamKrishna for your contributions here!

It's great to have SLURM compatibility. Unfortunately a couple of problems were also introduced, the main ones being: the proposed fix to run BLAST broke tests and local ANIb operation; breaking changes were made to the CLI; and SGE compatibility was broken.

I'm building on your changes in the pr_246 branch here to pull operation back in line with the expected operation and interface, and to ensure the test suite passes, so am closing this pull request.

widdowquinn
widdowquinn reviewed Jun 19, 2021
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SLURM integration works, but breaking changes are introduced to operation of the code, and to the CLI. I've pulled these changes into a new branch (pr_236) and will continue development from there.

@widdowquinn widdowquinn mentioned this pull request Sep 6, 2021
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enhancement something we'd like pyani to do that it doesn't already
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Add SLURM support
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@TSL-RamKrishna @widdowquinn