recipe mdmcleaner

A pipeline for the assessment, classification and refinement of microbial dark matter SAGs and MAGs

Homepage:

https://github.com/KIT-IBG-5/mdmcleaner

License:

GPL-3.0

Recipe:

/mdmcleaner/meta.yaml

package mdmcleaner

(downloads) docker_mdmcleaner

versions:

0.8.7-00.8.3-00.8.2-0

depends aragorn:

>=1.2.38

depends barrnap:

>=0.9

depends biopython:

>=1.78

depends blast:

>=2.10

depends diamond:

>=2.0.6

depends hmmer:

>=3.3.1

depends numpy:

>=1.19.2

depends prodigal:

>=2.6.3

depends python:

>=3.7

depends wget:

>=1.19

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 mdmcleaner

and update with::

   mamba update mdmcleaner

To create a new environment, run:

mamba create --name myenvname mdmcleaner

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/mdmcleaner:<tag>

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

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