recipe gff3toembl

Submitting annotated genomes to EMBL is a very difficult and time consuming process. This software converts GFF3 files from the most commonly use prokaryote annotation tool Prokka into a format that is suitable for submission to EMBL. It has been used to prepare more than 30% of all annotated genomes in EMBL/GenBank.

Homepage:

https://github.com/sanger-pathogens/gff3toembl/

License:

GNU GENERAL PUBLIC LICENSE

Recipe:

/gff3toembl/meta.yaml

package gff3toembl

(downloads) docker_gff3toembl

versions:

1.1.4-2,  1.1.4-1,  1.1.4-0

depends genometools-genometools:

depends python:

depends six:

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 gff3toembl

and update with::

   mamba update gff3toembl

To create a new environment, run:

mamba create --name myenvname gff3toembl

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/gff3toembl:<tag>

(see `gff3toembl/tags`_ for valid values for ``<tag>``)

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Link to this page

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