recipe cpat

Coding Potential Assessment Tool.

Homepage:

https://github.com/liguowang/cpat

Documentation:

https://cpat.readthedocs.io/en/latest

License:

GPL / GPL-2.0-or-later

Recipe:

/cpat/meta.yaml

Links:

doi: 10.1093/nar/gkt006, biotools: cpat, usegalaxy-eu: cpat

package cpat

versions:

3.0.5-4,  3.0.5-3,  3.0.5-2,  3.0.5-1,  3.0.5-0,  3.0.4-2,  3.0.4-1,  3.0.4-0,  2.0.0-4, 

3.0.5-4,  3.0.5-3,  3.0.5-2,  3.0.5-1,  3.0.5-0,  3.0.4-2,  3.0.4-1,  3.0.4-0,  2.0.0-4,  2.0.0-3,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.2.4-1,  1.2.4-0,  1.2.3-1,  1.2.3-0,  1.2.2-2

depends bx-python:

>=0.11.0,<0.12.0a0

depends libgcc:

>=13

depends numpy:

>=1.22.4,<2.0a0

depends pysam:

>=0.23.0,<0.24.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends r-base:

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 cpat

and update with::

   mamba update cpat

To create a new environment, run:

mamba create --name myenvname cpat

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/cpat:<tag>

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

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