recipe comebin

COMEBin allows effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning

Homepage:

https://github.com/ziyewang/COMEBin

License:

BSD

Recipe:

/comebin/meta.yaml

package comebin

(downloads) docker_comebin

versions:

1.0.4-0,  1.0.3-0,  1.0.2-0

depends atomicwrites:

1.4.0.*

depends bedtools:

2.30.0.*

depends biolib:

0.1.6.*

depends biopython:

1.76.*

depends bwa:

0.7.17.*

depends checkm-genome:

1.1.3.*

depends click:

8.0.4.*

depends fraggenescan:

1.31.*

depends hmmer:

3.1b2.*

depends hnswlib:

0.6.2.*

depends igraph:

0.9.9.*

depends joblib:

1.1.0.*

depends leidenalg:

0.8.10.*

depends matplotlib-base:

3.5.1.*

depends matplotlib-inline:

0.1.3.*

depends networkx:

2.6.3.*

depends numpy:

1.19.0.*

depends pandas:

1.3.5.*

depends pip:

22.0.4.*

depends pplacer:

1.1.alpha19.*

depends prodigal:

2.6.3.*

depends python:

3.7.*

depends python-dateutil:

2.8.2.*

depends python-fastjsonschema:

2.15.3.*

depends pytorch:

1.10.2.*

depends pyyaml:

6.0.*

depends samtools:

1.15.1.*

depends scanpy:

1.9.1.*

depends scikit-learn:

0.22.1.*

depends scipy:

1.7.3.*

depends seaborn:

0.12.1.*

depends setuptools:

59.5.0.*

depends tensorboard:

1.15.0.*

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 comebin

and update with::

   mamba update comebin

To create a new environment, run:

mamba create --name myenvname comebin

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/comebin:<tag>

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