recipe gnk_fastasort

A package to generate a GenomeNote ordered TSV of a genome.

Homepage:

https://github.com/sanger-tol/gnk_fastasort

License:

MIT

Recipe:

/gnk_fastasort/meta.yaml

This package uses can use either a SAMTOOLS FAIDX indexed genome or an API call to NCBI to retrieve a sequence report. This is then used to generate a preferred ordering of the genome as a TSV, which can then be used to re-order a pretextsnapshot or create a re-ordered fasta file using samtools faidx.

package gnk_fastasort

(downloads) docker_gnk_fastasort

versions:

0.1.0-0

depends python:

>=3.12

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 gnk_fastasort

and update with::

   mamba update gnk_fastasort

To create a new environment, run:

mamba create --name myenvname gnk_fastasort

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/gnk_fastasort:<tag>

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

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Link to this page

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