recipe ngscheckmate

Software package for identifying next generation sequencing (NGS) data files from the same individual.

Homepage:

https://github.com/parklab/NGSCheckMate

Documentation:

https://github.com/parklab/NGSCheckMate/blob/master/Documentation.pdf

License:

MIT / MIT

Recipe:

/ngscheckmate/meta.yaml

Links:

biotools: ngscheckmate

This version is built from a pull request which fixes a handful of known bugs.

package ngscheckmate

(downloads) docker_ngscheckmate

versions:

1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.1-0,  1.0.0-3,  1.0.0-1,  1.0.0-0

depends bcftools:

>=1.21,<2.0a0

depends bowtie:

>=1.3.1,<1.4.0a0

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends perl:

depends python:

>=3.12,<3.13.0a0

depends python_abi:

3.12.* *_cp312

depends r-base:

>=4

depends samtools:

>=1.21,<2.0a0

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 ngscheckmate

and update with::

   mamba update ngscheckmate

To create a new environment, run:

mamba create --name myenvname ngscheckmate

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/ngscheckmate:<tag>

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

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Link to this page

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