ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
481 stars 106 forks source link

Bump gpu docker to ubuntu 22 as Toil 7.0 seems to want Python version > 3.8 #1414

Closed glennhickey closed 2 weeks ago

glennhickey commented 2 weeks ago

The GPU docker image builder script failed for v2.8.3 at the very end when it verifies that cactus --help runs through

Traceback (most recent call last):
  File "/cactus/venv-cactus/bin/cactus", line 5, in <module>
    from cactus.progressive.cactus_progressive import main
  File "/cactus/venv-cactus/lib/python3.8/site-packages/cactus/progressive/cactus_progressive.py", line 20, in <module>
    from toil.lib.bioio import getTempFile
  File "/cactus/venv-cactus/lib/python3.8/site-packages/toil/lib/bioio.py", line 18, in <module>
    from toil.test import get_temp_file
  File "/cactus/venv-cactus/lib/python3.8/site-packages/toil/test/__init__.py", line 54, in <module>
    from backports import zoneinfo
ModuleNotFoundError: No module named 'backports'

As far as I can tell, this error comes from an incompatibility between Toil 7.0 and Python 3.8, which the GPU image was still pinned to. I think the GPU image being built on Ubuntu 20.04 dates back to Terra driver compatibility. This PR keeps Cuda at 11 (which should hopefully be compatible with the same drivers) but bumps up the image to Ubuntu 22.04.

Even though this patch is not part of the v2.8.3 tag, I used it (out of necessity) to build the GPU docker image for v2.8.3.

I think having to upgrade to Cuda 12 is probably inevitable in the next year or so, but I'll save that rabbit hole for a bit later.

To avoid further confusion, this PR also updates Cactus's minimum Python version to 3.9!

glennhickey commented 2 weeks ago

Note: This is fixed in Toil quite simply: https://github.com/DataBiosphere/toil/pull/4970

So I'm going to drop the Python 3.9 support requirement in Cactus from this PR. 3.8 can be supported either by downgrading Toil or running pip install backports.zoneinfo