recipe pcne

Estimates plasmid copy number from assembled genome.

Homepage:

https://github.com/riccabolla/PCNE

License:

MIT

Recipe:

/pcne/meta.yaml

package pcne

versions:

0.2.0-1,  0.2.0-0,  0.1.0-0

depends bash:

depends bc:

depends bedtools:

>=2.31.1

depends busco:

5.8.2.*

depends bwa:

>=0.7.19

depends r-base:

>=4.4.2

depends r-dplyr:

>=1.1.4

depends r-ggplot2:

>=3.5.1

depends r-readr:

>=2.1.5

depends samtools:

>=1.20

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 pcne

and update with::

   mamba update pcne

To create a new environment, run:

mamba create --name myenvname pcne

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/pcne:<tag>

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

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/pcne/README.html)