recipe bamm

Metagenomics-focused BAM file manipulation

Homepage:

https://github.com/Ecogenomics/BamM

License:

LGPL-3.0

Recipe:

/bamm/meta.yaml

package bamm

(downloads) docker_bamm

versions:
1.7.3-13,  1.7.3-12,  1.7.3-11,  1.7.3-10,  1.7.3-9,  1.7.3-8,  1.7.3-7,  1.7.3-6,  1.7.3-5, 

1.7.3-13,  1.7.3-12,  1.7.3-11,  1.7.3-10,  1.7.3-9,  1.7.3-8,  1.7.3-7,  1.7.3-6,  1.7.3-5,  1.7.3-4,  1.7.3-3,  1.7.3-2,  1.7.3-1,  1.7.3-0

depends bwa:

>=0.7.12

depends htslib:

>=1.17,<1.22.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends numpy:

depends python:

>=2.7,<2.8.0a0

depends python_abi:

2.7.* *_cp27mu

depends samtools:

>=1.3.1

depends zlib:

>=1.2.13,<1.3.0a0

requirements:

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 bamm

and update with::

   mamba update bamm

To create a new environment, run:

mamba create --name myenvname bamm

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/bamm:<tag>

(see `bamm/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/bamm/README.html)