khench/msa_envs repository overview

⁠Container repository for msa_envs

This container is meant as a support of the msa_pipeline⁠ by the Buckler lab and likely somewhat redundant with their original container⁠ (apscheben/msa_pipeline). For the initial building setup, please refer to the accompanying github repository msa_envs_build⁠.

The main motivation for this container was to include all conda environments needed for the pipeline, where all environments listed in the directory workflow/envs with the naming convention 'envs/{name}.yaml' -> msa_{name}, such that for example the conda environment specyfied within the file envs/align.yaml can be activated with conda activate msa_align. This was done so that the execution of the msa_pipeline can be seamlessly toggled between the usage of --use-conda and --use-singularity (as long as the container and environment names in the Snakefile in the rules/*.smk files are adjusted accordingly):

eg replace the original (workflow/rules/align.smk), line 8:

containerized: "docker://apscheben/msa_pipeline:latest"

with

containerized: "docker://khench/msa_envs:v0.1.1"

and eg lines 80-81:

    conda:
      '../envs/align.yaml'

with

    conda:
      'msa_align'

(and all other instances of conda environments accordingly).

⁠usage

To use the container, run for example:

podman run docker.io/khench/msa_envs:v0.1.1 which lastal