python-snakemake-skeleton

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A skeleton repository for Snakemake pipepline(s) and a python command-line toolkit.

Why this repo?

This the starting point for Fulcrum Genomics projects that contain Snakemake pipelines and a python toolkit.

This repo contains the following, in no particular order:

• a hello world snakefile in src/snakemake/hello_world.smk
  • this uses the onerror directive to better display rule errors, in particular the last file lines of the rule's log
• a python toolkit (clien-tools) in src/python/pyclient
  • uses defopt for arg parsing
  • has custom logging in core/logging.py
  • has utility methods to support the above onerror snakemake directive in pipeline/snakemake_utils.py
  • has a unit test to ensure the above snakefile is runnable and generally executes the expected rules in tests/test_hello_world.py. This also includes a utility method to support running and verifying snakemake in tests/util.py
  • supports multiple sub-commands in tools/__main__.py with some nice logging when a tool fails
  • a little hello world tool in tools/hello_world.py

Modifying this repo for a new client

This repo is a skeleton for Snakemake pipelines and a Python toolkit.

• [ ] Modify setup.py
• [ ] update conda-requirements-minimal.txt with minimal requirements for the client-tools toolkit
• [ ] update conda-requirements-test.txt with minimal requirements for the client-tools unit testing
• [ ] update pip-requirements.txt with minimal requirements for the client-tools (prefer conda)
• [ ] update src/python/pyclient source code (search for terms: PYCLIENT, pyclient, client-tools

Install client-tools

• Install conda

• Create the pyclient conda environment

mamba create -n pyclient \
  --override-channels -y \
  -c bioconda -c conda-forge -c defaults \
  --file conda-requirements-minimal.txt \
  --file conda-requirements-test.txt

• Activate the pyclient conda environment

conda activate pyclient

• Install all non-conda dependencies via pip

pip install -r pip-requirements.txt

• Install pyclient (in developer mode)

python setup.py develop

• Validate the install via the help message

client-tools -h

• Validate the snakemake install

snakemake --snakefile src/snakemake/hello_world.smk -j 1