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cucapra / pollen

generating hardware accelerators for pangenomic graph queries
MIT License
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`odgi` source confusion #74

Open anshumanmohan opened 1 year ago

anshumanmohan commented 1 year ago

Or, whose odgi is it anyway

  1. slow-odgi does not strictly need odgi if you just want to run/benchmark it. It does need odgi if you want to run the tests, and in that case you need the built-from-source odgi because the source code contains fixes that were made on our request and those fixes are not yet available on Bioconda.
  2. exine needs odgi, and in particular it needs odgi's Python bindings. The most reliable way we know to do this is via Bioconda, which is why we suggest this route in the Pollen readme.

This works, but is a little gross. I just wanted to put this down somewhere so it's not just me who knows this dirty secret 😅

I'll poke around some to see if I can reliably solve this via one single installation of odgi.

anshumanmohan commented 1 year ago

If #105 is okay-ed, we will no longer need the odgi Python bindings and this will go away for free.

sampsyo commented 1 year ago

Excellent.