recipe biopet

Biopet (Bio Pipeline Execution Toolkit) is the main pipeline development framework of the LUMC Sequencing Analysis Support Core team.

Homepage:

https://github.com/biopet/biopet

License:

https://github.com/biopet/biopet/blob/develop/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt

Recipe:

/biopet/meta.yaml

package biopet

(downloads) docker_biopet

versions:

0.9.0-2,  0.9.0-1,  0.9.0-0,  0.8.0-1,  0.8.0-0,  0.7.0-0

depends openjdk:

depends python:

depends r-argparse:

depends r-base:

depends r-ggplot2:

depends r-reshape:

requirements:

additional platforms:

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 biopet

and update with::

   mamba update biopet

To create a new environment, run:

mamba create --name myenvname biopet

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/biopet:<tag>

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