search

fedarko / strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
BSD 3-Clause "New" or "Revised" License
8 stars 1 forks source link

Fix build #8

Closed fedarko closed 2 years ago

fedarko commented 2 years ago

looks like moving the pysam(stats) install to conda from pip broke something. which is weird, because doing it the other way broke things on the cluster?

gotta figure out what dependencies are being messed up

update: as a hack, maybe try installing pysam(stats) before the rest of the conda dependencies, then filling in other stuff afterwards?

fedarko commented 2 years ago

Looks like pinning Python to 3.6 or 3.7 fixes this. The conda install fails with Python 3.8 and 3.9, but works with 3.6 and 3.7. (3.6 is the lowest we can go with Python because my code uses f-strings, which were introduced in 3.6.)

How does the install fail, specifically? It's hard to tell, but it looks like there are certain C dependencies that later versions of Python require -- but that pysam < 0.16 doesn't work with. I'm attaching the log, for reference.

log.txt

Maybe it's possible to figure out a way around this (if nothing else, by figuring out what to update for pysamstats to get it up to date with newer pysam versions), but for now it's easiest to just pin the Python versions and move on.