Metadata-Version: 2.1
Name: acanthophis
Version: 0.3.0
Summary: A comprehensive, opinionated plant variant calling pipeline in Snakemake
Home-page: https://github.com/kdm9/acanthophis
Author: Dr. K. D. Murray
Author-email: foss@kdmurray.id.au
Project-URL: Bug Tracker, https://github.com/kdm9/acanthophis/issues
Project-URL: Source, https://github.com/kdm9/acanthophis
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Unix Shell
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: natsort
Requires-Dist: snakemake

# Acanthophis

[![DOI](https://zenodo.org/badge/345496657.svg)](https://zenodo.org/badge/latestdoi/345496657)

A reusable, comprehensive, opinionated plant hologenomics and variant calling
pipeline in Snakemake

# Documentation

For documentation, see [./documentation.md](documentation.md). In summary:

```bash
# 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/
```



## About & Authors

This is an amalgamation of several pipelines developed between the [Weigel
Group, MPI DB, Tübingen, DE](https://weigelworld.org), the [Warthmann Group,
IAEA/FAO PBGL, Seibersdorf, AT](http://warthmann.com) and the [Borevitz Group,
ANU, Canberra, AU](https://borevitzlab.anu.edu.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.
