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Fix bug introdued with new memory environment variables #1309

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merged 1 commit into from
Mar 13, 2024

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glennhickey
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I hacked this logic (#1283, #1292) in when struggling with some T2T alignments on Slurm, but clearly didn't test it enough since it completely broke cactus on AWS/MESOS. The reason is that it's using (and int-casting) options.maxMemory and options.defaultMemory from Toil, which default to None on AWS/MESOS (but not single machine and slurm where I was testing).

Anyway, this PR should fix it, buy handling None values (and making sure that passed-in values are properly parsed).

@glennhickey glennhickey merged commit c82ce98 into master Mar 13, 2024
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