Metadata-Version: 2.1
Name: acanthophis
Version: 0.1.4
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
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/kdm9/acanthophis/issues
Description: # Acanthophis
        
        A reusable, comprehensive, opinionated plant variant calling pipeline in Snakemake
        
        Until I write the documentation, please see [the example workflow](example/).
        It should contain a fully working example workflow.
        
        ![Acanthophis, the most beautiful and badass of snakes](.github/logo.jpg)
        
        ## Installation & Use
        
        ```bash
        # 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](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, and Ilja Bezrukov, with contributions from others at the aforementioned institutes.
        
        
        # TODO:
        
        - [ ] break out more freebayes parameters to the config file
        - [ ] merge sample bams before doing markdups
        
Platform: UNKNOWN
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
