Package Recipe 'enrichm'

recipe enrichm

EnrichM is a toolbox for comparing the functional composition of population genomes.

Homepage:: https://github.com/geronimp/enrichM
License:: GPL3 / GPL-3.0-or-later
Recipe:: /enrichm/meta.yaml

package enrichm¶

Versions:

0.6.6-0, 0.6.5-0, 0.6.4-0, 0.6.3-0, 0.6.2-0, 0.5.0-0

Depends:

on biopython >=1.66
on diamond
on fuzzywuzzy >=0.18.0
on hmmer >=3.1b
on mcl >=14.137
on mmseqs2 >=2.23394
on moreutils
on numpy >=1.9.1
on openmpi
on pandas >=0.17.1
on parallel >=20180222
on prodigal >=2.6.3
on python >=3.6
on python-dateutil >=2.8.0
on r-base
on r-gridextra
on r-optparse
on scikit-learn
on scipy >=0.17.0
on seqmagick
on six >=1.10.0
on statsmodels >=0.8.0rc1
on tempdir >=0.7.1

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install enrichm

to add into an existing workspace instead, run:

pixi add enrichm

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install enrichm

Alternatively, to install into a new environment, run:

conda create -n envname enrichm

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/enrichm:<tag>

(see enrichm/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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/enrichm/README.html)