recipe genome_profiler

Prokaryotic genome and plasmid profiling pipeline.

Homepage:

https://github.com/Syrinx55/GenomeProfiler

Documentation:

https://github.com/Syrinx55/GenomeProfiler/blob/v0.4.2/README.md

License:

BSD / BSD-2-Clause-Patent

Recipe:

/genome_profiler/meta.yaml

package genome_profiler

versions:

0.4.2-0

depends abricate:

>=1.0.1

depends bio:

>=1.8

depends diamond:

depends ectyper:

depends integron_finder:

depends isescan:

depends lxml:

depends mash:

depends ncbi-datasets-cli:

depends pycurl:

depends python:

>=3.10

depends python-dotenv:

depends ratelimit:

depends requests-toolbelt:

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 genome_profiler

and update with::

   mamba update genome_profiler

To create a new environment, run:

mamba create --name myenvname genome_profiler

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/genome_profiler:<tag>

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

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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/genome_profiler/README.html)