Define conda channel in tljh_extra_user_conda_packages hook

[JudoWill]

Proposed change

Enable the definition of custom conda channels in the tljh_extra_user_conda_packages plugin hook. I often need to install conda packages from the bioconda, fastai, or local channels.

There is even a note on line 111 of tljh/conda.py about making this customizable. I'm not sure of the most elegant way to adjust the code or configuration option to make the feature possible.

I could imagine new hook that allows the plugin to define the conda channels to use during install.

Alternative options

There could be a hacky way to use the tljh_post_install hook to run a second conda install on the user environment, but this seems less ideal.

I also tried returning a list of conda packages from tljh_extra_user_conda_packages that prefixed the channels like so:

def tljh_extra_user_conda_packages():
    return ['-c', 'bioconda', 'snakemake']

which could add the channel to the conda command. However, line: 372 of tlhj/installer.py is

conda_packages = list(set(itertools.chain(*hook.tljh_extra_user_conda_packages())))

The set operation destroys the order. One could remove the set or replace it with a collections.OrderedDict to ensure the order is preserved while still de-duplicating. That would allow the proper command to be created

{conda} install -c conda-forge --json --prefix {abspath} -c bioconda snakemake

Who would use this feature?

Bioinformatics researchers who provision TLHJ as a teaching tool or sharable workstation.

This is similar to #779 which suggests allowing an env.yaml file for user requirements. It suggests that the same functionality is possible through plugins .... except if you need to define a new channel.

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