recipe vgp-processcuration

ProcessCurated - Toolkit for processing manually curated genome assemblies

Homepage:

https://github.com/vgl-hub/vgl-curation

Documentation:

https://github.com/vgl-hub/vgl-curation/blob/postcuration_1.0/README.md

License:

MIT / MIT

Recipe:

/vgp-processcuration/meta.yaml

ProcessCurated is a toolkit for processing manually curated genome assemblies. It reconciles AGP files manually curated in PretextView to rename, reorient, and sort assemblies in preparation for submission. The tool performs three main operations: correcting and splitting AGP files while assigning unlocalized sequences, assigning chromosome names to scaffolds, and reorienting and renaming sequences based on MashMap alignment data.

package vgp-processcuration

(downloads) docker_vgp-processcuration

versions:

1.0-0

depends biopython:

>=1.85

depends natsort:

>=8.4.0

depends pandas:

>=2.3

depends python:

>=3.9

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 vgp-processcuration

and update with::

   mamba update vgp-processcuration

To create a new environment, run:

mamba create --name myenvname vgp-processcuration

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/vgp-processcuration:<tag>

(see `vgp-processcuration/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda 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/vgp-processcuration/README.html)