recipe deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Homepage:

https://github.com/google/deepvariant

Documentation:

https://github.com/google/deepvariant/blob/v1.9.0/README.md

License:

BSD / BSD-3-Clause

Recipe:

/deepvariant/meta.yaml

package deepvariant

versions:

1.9.0-0,  1.8.0-0,  1.5.0-0,  1.4.0-0,  1.3.0-0,  1.2.0-0,  1.1.0-2,  1.1.0-1,  1.1.0-0, 

1.9.0-0,  1.8.0-0,  1.5.0-0,  1.4.0-0,  1.3.0-0,  1.2.0-0,  1.1.0-2,  1.1.0-1,  1.1.0-0,  1.0.0-3,  1.0.0-2,  1.0.0-1,  1.0.0-0,  0.10.0-4,  0.10.0-3,  0.10.0-2,  0.10.0-1,  0.10.0-0,  0.9.0-0,  0.8.0-0,  0.7.2-1,  0.7.2-0,  0.7.1-0,  0.7.0-0,  0.6.1-3,  0.6.1-2,  0.6.1-0,  0.6.0-0,  0.4.1-1,  0.4.1-0

depends absl-py:

depends altair:

depends boost-cpp:

depends contextlib2:

depends crcmod:

depends google-cloud-sdk:

depends htslib:

depends intervaltree:

depends mock:

depends numpy:

>=1.21.2

depends oauth2client:

depends openjdk:

11.0.*

depends parallel:

depends protobuf:

depends psutil:

depends python:

<3.11

depends requests:

depends scipy:

depends six:

depends tensorflow:

2.11.*

depends tensorflow-estimator:

2.11.*

requirements:

additional platforms:

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 deepvariant

and update with::

   mamba update deepvariant

To create a new environment, run:

mamba create --name myenvname deepvariant

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/deepvariant:<tag>

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

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