recipe vqsr_cnn

Variant quality score recalibration with Convolutional Neural Networks

Homepage:

https://broadinstitute.org/

License:

MIT

Recipe:

/vqsr_cnn/meta.yaml

package vqsr_cnn

versions:

0.0.194-0,  0.0.132-1,  0.0.132-0

depends biopython:

>=1.70

depends gatktool:

depends keras:

>=2.0

depends matplotlib:

>=2.1.2

depends numpy:

>=1.13.1

depends pysam:

>=0.13

depends python:

depends pyvcf:

>=0.6.8

depends scikit-learn:

>=0.19.1

depends scipy:

>=0.19.1

depends tensorflow:

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 vqsr_cnn

and update with::

   mamba update vqsr_cnn

To create a new environment, run:

mamba create --name myenvname vqsr_cnn

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/vqsr_cnn:<tag>

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

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