some cmalign subprocess udpates

[crosenth]

• quieting logging status messages
• piping cmalign output to logging
• defaulting cmalign # of cpus to 2
• added tmpdir argument for intermediate files

[cmccoy]

Hey Chris - thanks for this. A few thoughts, if it's not too annoying:

• Would you mind (re)basing this of fhcrc/master?
• Could --tmp be accomplished by setting TMPDIR in the environment? Seems equivalent, other than creating the directory.
• I think the default number of CPUs should be the same across cmalign and pplacer subprocesses.

[crosenth]

• done (i think)
• yes, removed the --tmp argument
• I believe the default for pplacer is also 2 (https://github.com/fhcrc/deenurp/blob/master/deenurp/wrap.py#L106)

[cmccoy]

The number of threads is overridden the only place pplacer is called (not that that's the best option); not so for cmalign.

[crosenth]

done

[cmccoy]

More generally, I think it we should either a) keep the parallelism as is (one process per taxon/OTU) or b) split into threads and processes, p concurrent tasks run, each with the option of using t threads. Task-level parallelism (pplacer, cmalign) would use the t threads; total parallelism would be t * p.

cc @nhoffman

[crosenth]

Thanks Connor. So we don't lose your last comment, wanna copy it to Issues and assign it to me or Noah?