recipe scalpel

Sensitive detection of INDELs (INsertions and DELetions)

Homepage:

http://scalpel.sourceforge.net/

License:

MIT

Recipe:

/scalpel/meta.yaml

package scalpel

versions:

0.5.4-8,  0.5.4-7,  0.5.4-6,  0.5.4-5,  0.5.4-4,  0.5.4-3,  0.5.4-2,  0.5.4-1,  0.5.4-0, 

0.5.4-8,  0.5.4-7,  0.5.4-6,  0.5.4-5,  0.5.4-4,  0.5.4-3,  0.5.4-2,  0.5.4-1,  0.5.4-0,  0.5.3-2,  0.5.3-1,  0.5.3-0,  0.5.1-3,  0.5.1-2,  0.5.1-1,  0.5.1-0

depends bamtools:

depends bcftools:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends perl:

depends samtools:

requirements:

additional platforms:

linux-aarch64

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 scalpel

and update with::

   mamba update scalpel

To create a new environment, run:

mamba create --name myenvname scalpel

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/scalpel:<tag>

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

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