recipe oncotator

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: 10.1002/humu.22771

package oncotator

(downloads) 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:

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 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:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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