recipe matam

MATAM is a software dedicated to the fast and accurate targeted assembly of short reads.

Homepage:

https://github.com/bonsai-team/matam

License:

AGPL-3.0

Recipe:

/matam/meta.yaml

Links:

doi: 10.1093/bioinformatics/btx644

package matam

versions:

1.6.1-1,  1.6.1-0,  1.6.0-3,  1.6.0-2,  1.6.0-1,  1.6.0-0

depends bzip2:

depends coreutils:

depends krona:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends numpy:

depends python:

>=3

depends rdptools:

depends samtools:

depends sga:

depends sortmerna:

2.1b.*

depends vsearch:

depends wget:

depends zlib:

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 matam

and update with::

   mamba update matam

To create a new environment, run:

mamba create --name myenvname matam

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/matam:<tag>

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

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