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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
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Update cov_filter.yml #131

Closed tsackton closed 8 months ago

tsackton commented 8 months ago

pin python to 3.10 to fix pyd4 issue

atigano commented 2 months ago

Hi Tim, I'm trying to install snpArcher and I'm running into the pyd4 issue. I tried a few things, including installing it with python 3.10 instead of 3.11, but nothing has worked. Did you find another solution since this last post? I've tried to install pyd4 manually but I got this error error: failed to run custom build command ford4-hts v0.3.9 (/gpfs/fs7/grdi/genarcc/wp3/annat/env/snparcher/d4-format/d4-hts)` and tried to install/fix the d4-hts but with no success.

cademirch commented 2 months ago

@atigano, yea there is something weird with the d4 htslib build script. Unfortunately the maintainer hasn't responded to issues regarding this. Even more frustrating, I have been able to build the cov_filter env on some servers, but I can't track down what is special about those servers. For now, you can set cov_filter: False in the config.yaml to run the workflow w/o the pyd4 dependency. We are discussing dropping pyd4 in #170.

atigano commented 2 months ago

Thank you, that worked!

On Thu, Apr 4, 2024 at 6:01 PM Cade Mirchandani @.***> wrote:

@atigano https://github.com/atigano, yea there is something weird with the d4 htslib build script. Unfortunately the maintainer hasn't responded to issues regarding this. Even more frustrating, I have been able to build the cov_filter env on some servers, but I can't track down what is special about those servers. For now, you can set cov_filter: False in the config.yaml to run the workflow w/o the pyd4 dependency. We are discussing dropping pyd4 in #170 https://github.com/harvardinformatics/snpArcher/pull/170.

— Reply to this email directly, view it on GitHub https://github.com/harvardinformatics/snpArcher/pull/131#issuecomment-2038560954, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJ6ZI7LVCAXGNKUO5DBHQTY3XZU7AVCNFSM6AAAAAA5WD2OCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZYGU3DAOJVGQ . You are receiving this because you were mentioned.Message ID: @.***>