recipe gbintk

GraphBin-Tk: assembly graph-based metagenomic binning toolkit

Homepage:

https://github.com/metagentools/gbintk

Documentation:

https://gbintk.readthedocs.io/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/gbintk/meta.yaml

GraphBin-Tk is a toolkit that combines assembly graph-based metagenomic bin-refinement and binning techniques GraphBin, GraphBin2 and MetaCoAG.

package gbintk

versions:

1.0.0-1,  1.0.0-0,  0.1.0-0

depends cairo:

depends cairocffi:

depends click:

depends cogent3:

depends fraggenescan:

depends graphbin:

depends graphbin2:

depends hmmer:

depends metacoag:

>=1.2.1

depends networkx:

depends numpy:

depends pandas:

depends pkg-config:

depends python:

>=3.10,<3.11.0a0

depends python-igraph:

depends python_abi:

3.10.* *_cp310

depends scipy:

depends tabulate:

depends tqdm:

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 gbintk

and update with::

   mamba update gbintk

To create a new environment, run:

mamba create --name myenvname gbintk

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/gbintk:<tag>

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

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