recipe clame

CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition.

Homepage:

https://github.com/andvides/CLAME

License:

GPL / GPL-3.0

Recipe:

/clame/meta.yaml

Links:

doi: 10.1186/s12864-018-5191-y

package clame

(downloads) docker_clame

versions:

1.0-1,  1.0-0

depends _openmp_mutex:

>=4.5

depends libgcc-ng:

>=7.3.0

depends libstdcxx-ng:

>=7.3.0

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 clame

and update with::

   mamba update clame

To create a new environment, run:

mamba create --name myenvname clame

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/clame:<tag>

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

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Link to this page

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