recipe cmat

ClinVar Mapping and Annotation Toolkit

Homepage:

https://github.com/EBIvariation/CMAT

License:

Apache-2.0

Recipe:

/cmat/meta.yaml

package cmat

versions:

3.1.3-0,  3.1.2-0,  3.1.1-0,  3.1.0-0

depends biopython:

1.77

depends coverage:

6.5.0

depends coveralls:

3.3.1

depends jsonschema:

3.2.0

depends nextflow:

>=21.10.0

depends numpy:

1.24.3

depends pandas:

1.5.3

depends pytest:

7.2.2

depends pytest-cov:

2.10.0

depends python:

>=3.8,<3.10

depends requests:

2.31.0

depends requests-mock:

1.8.0

depends retry:

0.9.2

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 cmat

and update with::

   mamba update cmat

To create a new environment, run:

mamba create --name myenvname cmat

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/cmat:<tag>

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

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