recipe discosnp

reference-free small variant caller for short read sequencing data

Homepage:

https://gatb.inria.fr/software/discosnp/

License:

GNU Affero General Public License v3.0

Recipe:

/discosnp/meta.yaml

Links:

biotools: discosnp, doi: 10.1093/nar/gkn000

package discosnp

versions:

2.6.2-4,  2.6.2-3,  2.6.2-2,  2.6.2-1,  2.6.2-0,  2.6.1-0,  2.5.4-1,  2.5.4-0,  2.4.4-0, 

2.6.2-4,  2.6.2-3,  2.6.2-2,  2.6.2-1,  2.6.2-0,  2.6.1-0,  2.5.4-1,  2.5.4-0,  2.4.4-0,  2.4.3-2,  2.4.3-1,  2.4.3-0,  2.3.0-7,  2.3.0-6,  2.3.0-5,  2.3.0-4,  2.3.0-3,  2.3.0-2,  2.3.0-1,  2.3.0-0,  2.2.10-1,  2.2.10-0

depends bwa:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends python:

>=3.0

depends short-read-connector:

depends zlib:

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 discosnp

and update with::

   mamba update discosnp

To create a new environment, run:

mamba create --name myenvname discosnp

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/discosnp:<tag>

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

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