recipe pybwa

Pybwa is a python module that makes it easy to align sequence data. It is a lightweight wrapper of bwa.

Homepage:

https://github.com/fulcrumgenomics/pybwa

Documentation:

https://pybwa.readthedocs.io/en/latest

License:

MIT / MIT

Recipe:

/pybwa/meta.yaml

package pybwa

(downloads) docker_pybwa

versions:

1.4.6-0,  1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.0-0,  1.3.4-0

depends fgpyo:

>=0.7.0

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends pysam:

>=0.22.1

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends typing-extensions:

>=3.7.4

requirements:

additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pybwa

and update with::

   mamba update pybwa

To create a new environment, run:

mamba create --name myenvname pybwa

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pybwa:<tag>

(see `pybwa/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pybwa/README.html)