Fix ssw-py issues #4
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…tible ssw-py calls
…tible ssw-py calls
inumanag
commented
Sep 25, 2022
| try: | ||
| from Cython.Build import cythonize | ||
| from Cython.Distutils import build_ext | ||
| except ImportError: |
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pyproject.toml should take care of these now, I guess
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Unfortunately, pyproject.toml does not take care of (hence, doc failling).
If this deleted part is recovered, will it affect your fix?
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It won't affect the fix--- please keep it in that case.
inumanag
commented
Sep 25, 2022
| from pysam import get_include as pysam_get_include | ||
|
|
||
| try: | ||
| import numpy |
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It seems that numpy is not used during the setup. Removing it as it can occasionally cause issues.
rawagiha
approved these changes
Sep 26, 2022
|
@ inumanag Thank you so much for your contribution. This is really helpful to alleviate the cumbersome installation issue. |
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Hi @rawagiha
Thank you for the indelpost---really nice piece of software!
We are extensively using indelpost in our pharmacogenomics suite Aldy. However, we have received lots of bug reports regarding the ssw-py dependency. ssw-py is quite hard to install, does not support newer Python versions, and is not compatible with ARM/M1 machines.
Here I integrated ssw-py directly into the indelpost tree and cleaned up various build issues with. ARM/M1 is also supported. We are using this version internally for now, and it would be great if you are able to merge it into the master branch.