:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'deepvariant' .. highlight: bash deepvariant =========== .. conda:recipe:: deepvariant :replaces_section_title: :noindex: 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 :license: MIT :recipe: /`deepvariant `_/`meta.yaml `_ .. conda:package:: deepvariant |downloads_deepvariant| |docker_deepvariant| :versions: .. raw:: html
1.5.0-01.4.0-01.3.0-01.2.0-01.1.0-21.1.0-11.1.0-01.0.0-31.0.0-2 ``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`` .. raw:: html
:depends absl-py: :depends altair: :depends boost: :depends contextlib2: :depends crcmod: :depends curl: ``>=7.87.0,<8.0a0`` :depends enum34: :depends google-cloud-sdk: :depends htslib: :depends intervaltree: :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends mock: :depends numpy: ``1.16.*`` :depends oauth2client: :depends openjdk: ``>=8,<9`` :depends parallel: :depends protobuf: :depends psutil: :depends python: ``>=3.6,<3.7.0a0`` :depends python_abi: ``3.6.* *_cp36m`` :depends requests: :depends scipy: :depends six: :depends tensorflow-estimator: ``2.0.*`` :depends tensorflow-gpu: ``2.0.*`` :depends unzip: :depends zlib: ``>=1.2.13,<1.3.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `deepvariant/tags`_ for valid values for ````) .. |downloads_deepvariant| image:: https://img.shields.io/conda/dn/bioconda/deepvariant.svg?style=flat :target: https://anaconda.org/bioconda/deepvariant :alt: (downloads) .. |docker_deepvariant| image:: https://quay.io/repository/biocontainers/deepvariant/status :target: https://quay.io/repository/biocontainers/deepvariant .. _`deepvariant/tags`: https://quay.io/repository/biocontainers/deepvariant?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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/deepvariant/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/deepvariant/README.html