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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
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Hail installation failes using mamba in empty environment. #38863

Open brechtmann opened 1 year ago

brechtmann commented 1 year ago

Currently for me the hail installation fails inside an empty environment with the following error.

mamba install  hail

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.1.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['hail']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
Could not solve for environment specs
Encountered problems while solving:
  - package hail-0.2.33-py36hf1ae8f4_1 requires tqdm 4.42.1, but none of the providers can be installed

The environment can't be solved, aborting the operation
brechtmann commented 1 year ago

running

mamba install hail --channel conda-forge --channel bioconda --strict-channel-priority

solved the above probem.

However, the resulting installation gave the following import error as jinja2 version 3.1.2 was installed.

>>> import hail                                               
Traceback (most recent call last):
        ...                                                                                                                      
ImportError: cannot import name 'Markup' from 'jinja2'

The recipe requires jinja2 < 3.1. https://github.com/bioconda/bioconda-recipes/blob/b94d1bd9a146dcf0ddcf4224ffd265f17ff0a489/recipes/hail/meta.yaml#L42

Further, the hail version is quite outdated. The newest on bioconda is 0.2.61. However, the current hail version is 0.2.107 (https://hail.is/docs/0.2/change_log.html)

Overall, installing hail from bioconda did not work for me, it would be great if the issues above could be resolved.

Hoeze commented 1 year ago

+1 on this. Maybe chance the title to Update hail package to v0.2.107 please