recipe tetyper

Typing of a specific transposable element (TE) of interest from paired-end sequencing data.

Homepage:

https://github.com/aesheppard/TETyper

License:

GPL-3.0

Recipe:

/tetyper/meta.yaml

Links:

doi: 10.1099/mgen.0.000232

package tetyper

(downloads) docker_tetyper

versions:

1.1-1,  1.1-0

depends bcftools:

depends biopython:

depends blast:

depends bwa:

depends pysam:

depends python:

depends pyvcf:

depends samtools:

depends spades:

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 tetyper

and update with::

   mamba update tetyper

To create a new environment, run:

mamba create --name myenvname tetyper

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/tetyper:<tag>

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

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Link to this page

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