recipe bowtie2

A fast and sensitive gapped read aligner.

Homepage:

https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Documentation:

https://github.com/BenLangmead/bowtie2/blob/v2.5.4/README.md

Developer docs:

https://github.com/BenLangmead/bowtie2

License:

GPL3 / GPL-3.0-or-later

Recipe:

/bowtie2/meta.yaml

Links:

biotools: bowtie2, doi: 10.1038/nmeth.1923, debian: bowtie2, usegalaxy-eu: bowtie2

package bowtie2

versions:

2.5.4-6,  2.5.4-5,  2.5.4-4,  2.5.4-3,  2.5.4-2,  2.5.4-1,  2.5.4-0,  2.5.3-1,  2.5.3-0, 

2.5.4-6,  2.5.4-5,  2.5.4-4,  2.5.4-3,  2.5.4-2,  2.5.4-1,  2.5.4-0,  2.5.3-1,  2.5.3-0,  2.5.2-0,  2.5.1-2,  2.5.1-1,  2.5.1-0,  2.5.0-0,  2.4.5-4,  2.4.5-3,  2.4.5-2,  2.4.5-1,  2.4.5-0,  2.4.4-1,  2.4.4-0,  2.4.3-0,  2.4.2-2,  2.4.2-1,  2.4.2-0,  2.4.1-3,  2.4.1-2,  2.4.1-1,  2.4.1-0,  2.3.5.1-0,  2.3.5-0,  2.3.4.3-1,  2.3.4.3-0,  2.3.4.2-0,  2.3.4.1-1,  2.3.4.1-0,  2.3.4-0,  2.3.3.1-0,  2.3.2-1,  2.3.0-1,  2.3.0-0,  2.2.8-2,  2.2.8-1,  2.2.8-0,  2.2.7-1,  2.2.7-0,  2.2.6-0,  2.2.5-8,  2.2.5-7,  2.2.5-6,  2.2.5-5,  2.2.5-4,  2.2.5-3,  2.2.5-2,  2.2.5-1,  2.2.4-8,  2.2.4-7,  2.2.4-6,  2.2.4-5,  2.2.4-4,  2.2.4-3,  2.2.4-2,  2.2.4-1,  2.2.4-0,  2.2.1-5,  2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-1,  2.2.1-0

depends _openmp_mutex:

>=4.5

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends perl:

depends python:

depends zstd:

>=1.5.7,<1.6.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 bowtie2

and update with::

   mamba update bowtie2

To create a new environment, run:

mamba create --name myenvname bowtie2

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/bowtie2:<tag>

(see `bowtie2/tags`_ for valid values for ``<tag>``)

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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/bowtie2/README.html)