:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'oncotator' .. highlight: bash oncotator ========= .. conda:recipe:: oncotator :replaces_section_title: :noindex: Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. :homepage: https://github.com/broadinstitute/oncotator :documentation: https://gatkforums.broadinstitute.org/gatk/categories/oncotator-documentation :license: Custom OSS :recipe: /`oncotator `_/`meta.yaml `_ :links: doi: :doi:`10.1002/humu.22771` .. conda:package:: oncotator |downloads_oncotator| |docker_oncotator| :versions: ``1.9.9.0-2``,  ``1.9.9.0-1``,  ``1.9.9.0-0`` :depends bcbio-gff: ``0.6.2`` :depends biopython: ``1.66`` :depends enum34: ``1.1.2`` :depends futures: :depends libgcc-ng: ``>=7.3.0`` :depends more-itertools: ``2.2`` :depends natsort: ``4.0.4`` :depends numpy: ``1.11.0`` :depends pandas: ``0.18.0`` :depends pysam: ``0.9.0`` :depends python: ``>=2.7,<2.8.0a0`` :depends python-memcached: ``1.57`` :depends pyvcf: ``0.6.8`` :depends shove: ``0.6.6`` :depends sqlalchemy: ``1.0.12`` :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 oncotator and update with:: mamba update oncotator To create a new environment, run:: mamba create --name myenvname oncotator 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/oncotator: (see `oncotator/tags`_ for valid values for ````) .. |downloads_oncotator| image:: https://img.shields.io/conda/dn/bioconda/oncotator.svg?style=flat :target: https://anaconda.org/bioconda/oncotator :alt: (downloads) .. |docker_oncotator| image:: https://quay.io/repository/biocontainers/oncotator/status :target: https://quay.io/repository/biocontainers/oncotator .. _`oncotator/tags`: https://quay.io/repository/biocontainers/oncotator?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/oncotator/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/oncotator/README.html