recipe tecount

A package to count read alignments on transposable elements subfamilies, families and classes.

Homepage:

https://github.com/bodegalab/tecount

License:

MIT

Recipe:

/tecount/meta.yaml

Links:

https: :https:`//doi.org/10.1038/s41588-021-00989-7`

package tecount

(downloads) docker_tecount

versions:

1.0.1-0,  1.0.0-0,  0.6.1-0,  0.6.0-0

depends bedtools:

>=2.30.0

depends pysam:

>=0.16.0.1

depends python:

>=3.7

depends samtools:

>=1.14

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 tecount

and update with::

   mamba update tecount

To create a new environment, run:

mamba create --name myenvname tecount

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/tecount:<tag>

(see `tecount/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/tecount/README.html)