recipe pysamstats

Calculate read mapping stats from SAM/BAM/CRAM

Homepage:

https://github.com/alimanfoo/pysamstats

License:

MIT

Recipe:

/pysamstats/meta.yaml

Links:

biotools: pysamstats

package pysamstats

(downloads) docker_pysamstats

versions:
1.1.2-15,  1.1.2-14,  1.1.2-13,  1.1.2-12,  1.1.2-11,  1.1.2-10,  1.1.2-9,  1.1.2-8,  1.1.2-7, 

1.1.2-15,  1.1.2-14,  1.1.2-13,  1.1.2-12,  1.1.2-11,  1.1.2-10,  1.1.2-9,  1.1.2-8,  1.1.2-7,  1.1.2-6,  1.1.2-5,  1.1.2-4,  1.1.2-3,  1.1.2-2,  1.1.2-1,  1.1.2-0,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.24.3-0,  0.24.2-1,  0.24.0-0

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends numpy:

depends pysam:

>=0.23.0,<0.23.1.0a0

depends pysam:

>=0.23.0,<0.24.0a0

depends pytables:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends zlib:

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 pysamstats

and update with::

   mamba update pysamstats

To create a new environment, run:

mamba create --name myenvname pysamstats

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/pysamstats:<tag>

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

Download stats

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/pysamstats/README.html)