recipe transindel

transIndel is used to detect indels (insertions and deletions) from DNA-seq or RNA-seq data by parsing chimeric alignments from BWA-MEM..

Homepage:

https://github.com/cauyrd/transIndel

License:

GPL3 / GNU General Public License v3 or later (GPLv3+)

Recipe:

/transindel/meta.yaml

package transindel

(downloads) docker_transindel

versions:

2.0-0,  1.0-2,  1.0-1,  1.0-0

depends htseq:

>=0.6.1

depends pysam:

>=0.13.0

depends python:

>=3.8

depends samtools:

>=1.0

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 transindel

and update with::

   mamba update transindel

To create a new environment, run:

mamba create --name myenvname transindel

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/transindel:<tag>

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