import plink-ng as a git dependency
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Mgymrek docs admixsim
to support plink-ng as a git dependency of the tool
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Looks like the readthedocs build failed because python-poetry/poetry-core#288 hasn't been merged in yet. And we will eventually want python-poetry/poetry-core#300 and python-poetry/poetry#5172 . The git url gets resolved to this instead of this (notice the equal sign after Update |
Initial functionality for admixture simulator and visualization
Feat/vcf output
Feat/vcf output
minor cleanups to simgenotype output messages
Feat/vcf output
docs: add apoe haplotype example
Added SAMPLE Format Field
Fixed issue in test_outputvcf.py
Merged
to support plink-ng as a git dependency of the tool
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ok, I just rebased and updated the pyproject file to require 1.1.0b1 But the readthedocs build still failed it looks like we'll still need python-poetry/poetry-core#300 in order to get this to work :( |
aryarm
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Jul 21, 2022
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closing in favor of #68 |
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Compared to VCFs, PLINK files are a much more efficient format for storing and working with GWAS datasets. Reading from PLINK files takes seconds, while I've estimated that reading from VCFs can take half an hour for even the small datasets we want to work with. We'll eventually want to list the Python API for
plink-ng(akapgenlib) as a dependency of this tool, so that we can properly support reading and writing PLINK files. Currently our code just assumes this dependency is installed instead of installing it automatically viapoetry.Unfortunately,
pgenlibhas not yet been published to PyPi, so we'll have to install it directly from the Github repo in the subdirectory that it lives in.poetry-coreadded support for installing git packages from subdirectories in v1.1.0a7 (yesterday, on 3/5/22). So this PR addspgenlibto the pyproject.toml file using the new syntax and updatespoetryandpoetry-coreto support installing it.