recipe survindel2

A CNV caller for Illumina paired-end WGS data.

Homepage:

https://github.com/kensung-lab/SurVIndel2

License:

GPL-3.0-only

Recipe:

/survindel2/meta.yaml

SurVIndel2 is a fast and accurate CNV caller for Illumina paired-end WGS data.

package survindel2

versions:

1.1.3-0

depends htslib:

>=1.20,<1.21.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends numpy:

depends pyfaidx:

>=0.5.9.1

depends pysam:

>=0.16.0.1

depends scikit-learn:

>=1.2.2

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 survindel2

and update with::

   mamba update survindel2

To create a new environment, run:

mamba create --name myenvname survindel2

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/survindel2:<tag>

(see `survindel2/tags`_ for valid values for ``<tag>``)

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