recipe sambamba

Tools for working with SAM/BAM data.

Homepage:

https://github.com/biod/sambamba

Documentation:

https://lomereiter.github.io/sambamba/docs/sambamba-view.html

License:

GPL2 / GPL-2.0-only

Recipe:

/sambamba/meta.yaml

Links:

doi: 10.1093/bioinformatics/btv098, biotools: sambamba, usegalaxy-eu: sambamba_flagstat, usegalaxy-eu: sambamba_markdup, usegalaxy-eu: sambamba_merge, usegalaxy-eu: sambamba_sort

package sambamba

(downloads) docker_sambamba

versions:
1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0-1,  1.0-0,  0.8.2-2,  0.8.1-1, 

1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0-1,  1.0-0,  0.8.2-2,  0.8.1-1,  0.8.1-0,  0.8.0-0,  0.7.1-3,  0.7.1-2,  0.7.1-1,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.9-0,  0.6.8-2,  0.6.8-1,  0.6.8-0,  0.6.6-2,  0.6.6-1,  0.6.6-0,  0.6.5-0,  0.6.3-0,  0.6.2-0,  0.6.1-0,  0.5.9-1,  0.5.9-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc:

>=13

depends liblzma:

>=5.6.4,<6.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends lz4-c:

>=1.9.3,<1.10.0a0

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 sambamba

and update with::

   mamba update sambamba

To create a new environment, run:

mamba create --name myenvname sambamba

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/sambamba:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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