recipe gempipe

gempipe is a tool for the reconstruction of strain-specific genome-scale metabolic models.

Homepage:

https://github.com/lazzarigioele/gempipe

Documentation:

https://gempipe.readthedocs.io/

License:

GPL3 / GPL-3.0-only

Recipe:

/gempipe/meta.yaml

package gempipe

(downloads) docker_gempipe

versions:
1.37.4-0,  1.37.3-0,  1.37.0-0,  1.36.0-0,  1.35.5-0,  1.35.4-0,  1.35.3-0,  1.35.2-0,  1.35.1-0, 

1.37.4-0,  1.37.3-0,  1.37.0-0,  1.36.0-0,  1.35.5-0,  1.35.4-0,  1.35.3-0,  1.35.2-0,  1.35.1-0,  1.35.0-0,  1.34.2-0,  1.34.1-0,  1.34.0-0,  1.33.4-0,  1.33.3-0,  1.33.2-0,  1.33.1-0,  1.33.0-0

depends biopython:

>=1.80

depends blast:

>=2.12.0

depends busco:

>=5.4.0

depends cd-hit:

>=4.8.1

depends cobra:

>=0.29

depends diamond:

>=2.0.15

depends eggnog-mapper:

>=2.1.7

depends ipython:

>=8.7.0

depends matplotlib-base:

>=3.7.0

depends ncbi-genome-download:

>=0.3.3

depends openpyxl:

>=3.1.0

depends pandas:

>=2.0.0

depends pigz:

>=2.5

depends prodigal:

>=2.6.3

depends prokka:

>=1.14.6

depends python:

>=3.9

depends scikit-learn:

>=1.3.0

depends scipy:

>=1.10.0

depends seaborn:

>=0.13.0

depends seqkit:

>=2.2.0

requirements:

additional platforms:

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 gempipe

and update with::

   mamba update gempipe

To create a new environment, run:

mamba create --name myenvname gempipe

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/gempipe:<tag>

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