recipe kmerinshort

KmerInShort counts kmers from a fasta/fastq file or list of files, and outputs results in a text file. It is limited to short kmers (k<15). It is a part of the FEELnc pipeline (V.Wucher et al.)

Homepage:

https://github.com/rizkg/KmerInShort

License:

aGPL v3

Recipe:

/kmerinshort/meta.yaml

package kmerinshort

(downloads) docker_kmerinshort

versions:

1.0.1-1,  1.0.1-0

depends zlib:

>=1.2.11,<1.3.0a0

requirements:

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 kmerinshort

and update with::

   mamba update kmerinshort

To create a new environment, run:

mamba create --name myenvname kmerinshort

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/kmerinshort:<tag>

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

Download stats

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/kmerinshort/README.html)