A comprehensive, opinionated plant variant calling pipeline in Snakemake

These details have not been verified by PyPI

Project links

Development Status
- 4 - Beta
Environment
- Console
Intended Audience
- Science/Research
License
- OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Operating System
- OS Independent
Programming Language
- Python :: 3
- Unix Shell
Topic
- Scientific/Engineering :: Bio-Informatics

Project description

Acanthophis

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

Until I write the documentation, please see the example workflow. It should contain a fully working example workflow.

Acanthophis, the most beautiful and badass of snakes

Installation & Use

# create conda env, activate it
conda create -n someproject python snakemake pip
conda activate someproject

# install acanthophis itself
pip install acanthophis

# generate boilerplate
acanthophis-init /path/to/someproject/

# edit config.yml to suit your project
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, 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, and Ilja Bezrukov, with contributions from others at the aforementioned institutes.

Project details

These details have not been verified by PyPI

Project links

Development Status
- 4 - Beta
Environment
- Console
Intended Audience
- Science/Research
License
- OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Operating System
- OS Independent
Programming Language
- Python :: 3
- Unix Shell
Topic
- Scientific/Engineering :: Bio-Informatics

Release history Release notifications | RSS feed

1.1.0

Aug 26, 2024

1.0.0

Mar 7, 2024

0.3.2

Jan 23, 2024

0.3.1

Jan 18, 2024

0.3.0

Jan 9, 2024

0.2.0

May 6, 2022

This version

0.1.17

May 6, 2022

0.1.16

Sep 9, 2021

0.1.15

Sep 8, 2021

0.1.14

Jun 28, 2021

0.1.13

Jun 22, 2021

0.1.12

Jun 17, 2021

0.1.10

May 28, 2021

0.1.6

May 28, 2021

0.1.4

Apr 7, 2021

0.1.3

Mar 11, 2021

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