recipe rfplasmid

RFPlasmid predicts plasmid contigs from assemblies using single copy marker genes, plasmid genes, and kmers.

Homepage:

https://github.com/aldertzomer/RFPlasmid

License:

GPL / GNU General Public License v3 (GPL-3.0)

Recipe:

/rfplasmid/meta.yaml

package rfplasmid

(downloads) docker_rfplasmid

versions:

0.0.18-0,  0.0.17-0,  0.0.16-0,  0.0.15-0

depends biopython:

depends checkm-genome:

depends diamond:

depends kmer-jellyfish:

depends pandas:

depends pysam:

>=0.15.3

depends python:

>=3.6

depends r-randomforest:

depends wget:

depends zlib:

>=1.2.11,<1.3.0a0

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 rfplasmid

and update with::

   mamba update rfplasmid

To create a new environment, run:

mamba create --name myenvname rfplasmid

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/rfplasmid:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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