Explicitly define conda environments

[ManavalanG]

Conda environments are currently implicitly defined with just the most high-level dependencies mentioned. This has led to issues in the past:

• https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/pipelines/quac/-/issues/47
• https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/pipelines/small_variant_caller_pipeline/-/issues/41

I suspect this will be a bigger issue as time goes by and new version of implicit dependencies become available. So specifying the exact dependency is a good idea to work around this issue.

[ManavalanG]

All dependencies can be identified from the existing conda environment. Here I used conda envs created by snakemake (for quac) with this script:

#!/usr/bin/env bash
set -euo pipefail

ml reset
ml Anaconda3

OUT_DIR="data/test"
mkdir -p $OUT_DIR
SNAKEMAKE_CONDA_DIRPATH="/path/to/quac/1.0/.snakemake/conda"

for conda_env in $(ls -d ${SNAKEMAKE_CONDA_DIRPATH}/*/)
do
    echo $conda_env
    env_dirpath=$(dirname $conda_env)
    env_name=$(basename $conda_env)
    echo $env_name
    
    cp ${env_dirpath}/${env_name}.yaml ${OUT_DIR}/${env_name}.yaml

    set +eu     # see https://github.com/conda/conda/issues/8186#issuecomment-532874667
    conda activate ${env_dirpath}/${env_name}
    set -eu     # https://github.com/conda/conda/issues/8186#issuecomment-532874667
    conda env export > ${OUT_DIR}/${env_name}_exported.yaml
    sleep 5
done

[ManavalanG]

mentioned in commit 6ddf6d9b85f6a289c1bbd94bed5bf1d564393755

[ManavalanG]

mentioned in commit 544a7f6df319c386f4deaa8a145c6e9f5fe5f3f8

[ManavalanG]

mentioned in commit 92db1d1