recipe plasann

A tool for plasmid annotation and visualization

Homepage:

https://github.com/ajlopatkin/PlasAnn

License:

MIT / MIT

Recipe:

/plasann/meta.yaml

A comprehensive tool for annotating plasmid sequences, identifying coding sequences, detecting origins of replication and transfer, and generating plasmid maps.

For Mac (Apple Silicon) users, please install these additional dependencies: - brew install blast - brew install brewsci/bio/prodigal

Please ensure both tools are available in your PATH before running PlasAnn.

package plasann

(downloads) docker_plasann

versions:

1.0.8-0,  1.0.3-0,  1.0.1-0

depends biopython:

>=1.78

depends blast:

depends gdown:

>=4.0.0

depends matplotlib-base:

>=3.0.0

depends pandas:

>=1.0.0

depends prodigal:

depends pycirclize:

>=0.1.0

depends python:

>=3.7

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 plasann

and update with::

   mamba update plasann

To create a new environment, run:

mamba create --name myenvname plasann

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/plasann:<tag>

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

Notes

This package requires external dependencies (BLAST and Prodigal) for Apple Silicon Macs which must be installed separately due to platform compatibility issues.

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

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