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:

0.9-0,  0.8-1,  0.8-0,  0.7-0

depends biopython:

1.84.*

depends blas:

1.0 mkl

depends dill:

0.3.7.*

depends h5py:

3.10.0.*

depends matplotlib:

3.8.2.*

depends numpy:

1.26.2.*

depends pandas:

2.1.3.*

depends pip:

23.3.1.*

depends pymc:

5.10.1.*

depends pysam:

0.22.0.*

depends pytensor:

2.18.3.*

depends python:

3.10.13.*

depends pytorch:

2.1.0 *mkl*100

depends pytorch-lightning:

2.4.0.*

depends pyvcf:

0.6.8.*

depends r-backports:

1.4.1.*

depends r-base:

4.3.1.*

depends r-data.table:

1.14.8.*

depends r-dplyr:

1.1.3.*

depends r-getopt:

1.20.4.*

depends r-ggplot2:

3.4.4.*

depends r-gplots:

3.1.3.*

depends r-gsalib:

2.2.1.*

depends r-optparse:

1.7.3.*

depends scikit-learn:

1.3.2.*

depends scipy:

1.11.4.*

depends tqdm:

4.66.1.*

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

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