recipe bwakit

A self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping

Homepage:

https://github.com/lh3/bwa/tree/master/bwakit

License:

GPLv3

Recipe:

/bwakit/meta.yaml

package bwakit

versions:

0.7.18.dev1-0,  0.7.17.dev1-1,  0.7.17.dev1-0,  0.7.15-3,  0.7.15-2,  0.7.15-1,  0.7.15-0,  0.7.12-0

depends bwa:

0.7.18

depends fermi2:

r170

depends htsbox:

r315

depends k8:

depends perl:

depends ropebwt2:

r187

depends samblaster:

0.1.20

depends samtools:

>=1.3

depends seqtk:

r82

depends trimadap:

r2

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 bwakit

and update with::

   mamba update bwakit

To create a new environment, run:

mamba create --name myenvname bwakit

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/bwakit:<tag>

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

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Link to this page

Render an 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/bwakit/README.html)