Metadata-Version: 2.1
Name: sourmash
Version: 4.0.0rc2
Summary: tools for comparing DNA sequences with MinHash sketches
Home-page: https://github.com/dib-lab/sourmash
Author: Luiz Irber, Harriet Alexander, Olga Botvinnik, Phillip Brooks, Laurent Gautier, Tim Head, Lisa K. Johnson, Fabian Klötzl, Katrin Leinweber, Ivan Ogasawara, N. Tessa Pierce, Andreas Sjödin, Connor T. Skennerton, Daniel Standage, S. Joshua Swamidass, Connor Tiffany, Erik Young, C. Titus Brown
Author-email: titus@idyll.org
Maintainer: Luiz Irber, C. Titus Brown
Maintainer-email: lcirberjr@ucdavis.edu, titus@idyll.org
License: BSD 3-clause
Project-URL: Documentation, https://sourmash.readthedocs.io
Project-URL: CI, https://github.com/dib-lab/sourmash/actions
Project-URL: Source, https://github.com/dib-lab/sourmash
Project-URL: Tracker, https://github.com/dib-lab/sourmash/issues
Description: # sourmash
        
        Quickly search, compare, and analyze genomic and metagenomic data sets.
        
        [![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)
        [![Build Status](https://github.com/dib-lab/sourmash/workflows/Python%20tests/badge.svg)](https://github.com/dib-lab/sourmash/actions/)
        [![Bioconda install](https://img.shields.io/conda/dn/bioconda/sourmash.svg?style=flag&label=Bioconda)](https://anaconda.org/bioconda/sourmash)
        <a href="https://pypi.org/project/sourmash/"><img alt="PyPI" src="https://badge.fury.io/py/sourmash.svg"></a>
        [![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
        [![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027)
        <a href="https://github.com/dib-lab/sourmash/blob/latest/LICENSE"><img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg"></a>
        
        <p align="center"><img src="https://raw.githubusercontent.com/dib-lab/sourmash/latest/doc/_static/logo.png" height="256" /></p>
        
        Usage:
        
            sourmash sketch dna *.fq.gz
            sourmash compare *.sig -o distances.cmp -k 31
            sourmash plot distances.cmp
        
        sourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.
        
        The latest major release is sourmash v4, which has several
        command-line and Python incompatibilities with previous
        versions. Please
        [visit our migration guide](https://sourmash.readthedocs.io/en/latest/support.html#migrating-from-sourmash-v3-x-to-sourmash-4-x)
        to upgrade!
        
        ----
        
        The name is a riff off of [Mash](https://github.com/marbl/Mash),
        combined with @ctb's love of whiskey.
        ([Sour mash](https://en.wikipedia.org/wiki/Sour_mash) is used in
        making whiskey.)
        
        Primary authors: [C. Titus Brown](mailto:titus@idyll.org) ([@ctb](http://github.com/ctb)) and [Luiz C. Irber, Jr](mailto:sourmash@luizirber.org) ([@luizirber](http://github.com/luizirber)).
        
        sourmash was initially developed by the
        [Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the
        [UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu),
        and now includes contributions from the global research and developer
        community.
        
        ## Installation
        
        We recommend using bioconda to install sourmash:
        
        ```
        conda install -c conda-forge -c bioconda sourmash
        ```
        This will install the latest stable version of sourmash 4.
        
        You can also use pip to install sourmash:
        
        ```
        pip install sourmash
        ```
        
        A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html).
        
        ### Requirements
        
        sourmash runs under Python 3.7 and later.  The base
        requirements are screed, cffi, numpy, matplotlib, and scipy.  Conda
        (see below) will install everything necessary, and is our recommended
        installation method.
        
        ### Installation with conda
        
        Bioconda is a channel for the
        [conda](http://conda.pydata.org/docs/intro.html) package manager with
        a focus on bioinformatics software. After
        [installing conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/),
        you can install sourmash by running:
        
        ```bash
        $ conda create -n sourmash_env -c conda-forge -c bioconda sourmash python=3.7
        $ source activate sourmash_env
        $ sourmash --help
        ```
        
        which will install
        [the latest released version](https://github.com/dib-lab/sourmash/releases).
        
        ## Support
        
        Please ask questions and files issues
        [on Github](https://github.com/dib-lab/sourmash/issues).
        
        ## Development
        
        Development happens on github at
        [dib-lab/sourmash](https://github.com/dib-lab/sourmash).
        
        sourmash is developed in Python and Rust, and you will need a Rust
        environment to build it; see [the developer notes](doc/developer.md)
        for our suggested development setup.
        
        After installation, `sourmash` is the main command-line entry point;
        run it with `python -m sourmash`, or do `pip install -e /path/to/repo` to
        do a developer install in a virtual environment.
        
        The `sourmash/` directory contains the Python library and command-line interface code.
        
        The `src/core/` directory contains the Rust library implementing core
        functionality.
        
        Tests require py.test and can be run with `make test`.
        
        Please see [the developer notes](doc/developer.md) for more information
        on getting set up with a development environment.
        
        ----
        
        CTB
        Feb 2021
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Environment :: MacOS X
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown; charset=UTF-8
Provides-Extra: test
Provides-Extra: demo
Provides-Extra: doc
Provides-Extra: storage
Provides-Extra: all
