A reusable, comprehensive, opinionated Snakemake pipeline for plant-microbe genomics and plant variant calling.
For documentation, see ./documentation.md. In summary:
# create conda env, activate it
mamba create -n someproject python snakemake pip natsort
mamba activate someproject
# Install acanthophis itself
pip install acanthophis
# Generate a workspace. This copies all files the workflow will need to your
# workspace directory.
acanthophis-init /path/to/someproject/
# Edit config.yml to suit your project. Hopefully this config file documents
# all options available in an understandable fashion. If not, please raise an
# issue on github.
vim config.yml
# Run snakemake
snakemake -j 16 -p --use-conda --conda-frontend mamba --ri
# Or on a cluster, see acanthophis-init --list-available-profiles
snakemake --profile ./ebio-cluster/While snakemake and Acanthophis are cross-platform, most of the underlying tools are only packaged for and/or only operate on Linux x68_64. Therefore, I only support users on Linux systems. In theory, everything should run on OSX or WSL, but the vast majority of users will want to utilise a high performance linux workstation (at least, probably more likely a cluster).
For running tests, see ./tests/README.md.
If you have anything (advice, docs, code) you'd like to contribute, pull requests are more than welcome. Please discuss any major contribution in a new issue before implementing it, to avoid wasted effort.
If you need any assistance, or have other questions or comments, please make an issue on github, or open a discussion. Unfortunately both need an account on github, so alternatively you can email me (foss <usual email symbol> kdmurray.id.au).
This is an amalgamation of several pipelines developed between the Weigel Group, MPI DB, Tübingen, DE, the Warthmann Group, IAEA/FAO PBGL, Seibersdorf, AT and the Borevitz Group, ANU, Canberra, AU. This amalgamation authored by Dr. K. D. Murray, original code primary by K. D. Murray, Norman Warthmann, with contributions from others at the aforementioned institutes.