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Use Mamba in install instructions #96

Merged
merged 2 commits into from
Nov 7, 2022
Merged

Use Mamba in install instructions #96

merged 2 commits into from
Nov 7, 2022

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christinehc
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Changelog:

  • Modify documentation to use Mamba for environment building (Conda has been observed to take ~1h+ vs. minutes for Mamba)
  • Add pip installation instructions to docs for pip users. (Note: pip installation is not recommended, which is noted as such in the docs)
  • Update environment specs to fix tabulate==0.8.10 (see: known issue with snakemake and newer tabulate versions)

There is a known issue with newer versions of tabulate that result in `AttributeError: 'str' object has no attribute 'name'` (see cov-lineages/pangolin#489). To resolve this error, environment specs have been modified to specify tabulate==0.8.10.
Previous installation instructions suggested Conda to handle environment building, dependencies, etc. The speed of conda environment solving is a known issue, so Mamba has been recommended instead, and the documentation has been updated accordingly.
@christinehc christinehc added the documentation Improvements or additions to documentation label Nov 5, 2022
@christinehc christinehc merged commit ef65578 into main Nov 7, 2022
@christinehc christinehc deleted the install branch November 7, 2022 16:59
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