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dermestid / bold-phylodiv-scripts

Scripts to calculate phylodiversity and its distribution from BOLD DNA barcode data.
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Do alignment in parallel #55

Closed dermestid closed 3 years ago

dermestid commented 3 years ago

Some other parts of the code are easily parallelizable too.

Something to note: parallelism should have a setting to switch it on or off, since I hear php's threading isn't supported on web servers.

dermestid commented 3 years ago

Also consider use of k-mer method instead of aligning then getting a distance matrix.

dermestid commented 3 years ago

Turns out that there are multiple ways to do multitasking in php, and the library solutions (e.g. pthreads) require specific php installation parameters. The simplest way to do it seems to be to let the OS handle it and ask it to exec Clustal in the background, and wait until the status shows completion for all jobs.