recipe gcnvkernel

Python package to support GATK gCNV calling.

Homepage:

https://www.broadinstitute.org/gatk/

Developer docs:

https://github.com/broadinstitute/gatk

License:

BSD / BSD-3-Clause

Recipe:

/gcnvkernel/meta.yaml

package gcnvkernel

(downloads) docker_gcnvkernel

versions:

0.8-1,  0.8-0,  0.7-0

depends biopython:

1.76.*

depends dill:

0.3.4.*

depends h5py:

2.10.0.*

depends intel-openmp:

depends keras:

2.2.4.*

depends matplotlib:

3.2.1.*

depends mkl:

2019.5.*

depends mkl-service:

2.3.0.*

depends numpy:

1.17.5.*

depends pandas:

1.0.3.*

depends pip:

21.3.1.*

depends pymc3:

3.1.*

depends pysam:

0.15.3.*

depends python:

3.6.10.*

depends pyvcf:

0.6.8.*

depends r-backports:

1.1.10.*

depends r-base:

3.6.2.*

depends r-data.table:

1.12.8.*

depends r-dplyr:

0.8.5.*

depends r-getopt:

1.20.3.*

depends r-ggplot2:

3.3.0.*

depends r-gplots:

3.0.3.*

depends r-gsalib:

2.1.*

depends r-optparse:

1.6.4.*

depends scikit-learn:

0.23.1.*

depends scipy:

1.0.0.*

depends tensorflow:

<2

depends theano:

1.0.4.*

depends typing_extensions:

4.1.1.*

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 gcnvkernel

and update with::

   mamba update gcnvkernel

To create a new environment, run:

mamba create --name myenvname gcnvkernel

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/gcnvkernel:<tag>

(see `gcnvkernel/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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