recipe consplice

The Constrained Splicing (ConSplice) python module

Homepage:

https://github.com/mikecormier/ConSplice

License:

MIT

Recipe:

/consplice/meta.yaml

ConSplice is a python module used to (1) model the splicing constraint in the human genome, and (2) an ensembl machine learning metric to score genetic variants for pathogenic splicing.

package consplice

versions:

0.0.6-0

depends bcftools:

depends biopython:

depends cyvcf2:

depends gsort:

depends gsort:

>=0.1.4

depends htslib:

depends interlap:

depends ncls:

0.0.53.*

depends numpy:

depends pandas:

depends pyfaidx:

depends pyranges:

0.0.92.*

depends pysam:

depends python:

depends pyyaml:

depends scikit-learn:

depends scipy:

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 consplice

and update with::

   mamba update consplice

To create a new environment, run:

mamba create --name myenvname consplice

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/consplice:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/consplice/README.html)