recipe wakhan

A tool to analyze haplotype-specific chromosome-scale somatic copy number aberrations and aneuploidy using long reads

Homepage:

https://github.com/KolmogorovLab/Wakhan

License:

MIT / MIT

Recipe:

/wakhan/meta.yaml

package wakhan

versions:

0.1.1-0

depends bcftools:

>=1.14

depends numpy:

depends pandas:

depends parse-vcf:

depends plotly:

depends pyfaidx:

depends pysam:

depends python:

>=3.7

depends python-kaleido:

depends ruptures:

depends samtools:

>=1.14

depends scikit-learn:

1.2.0

depends scipy:

1.9.2

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 wakhan

and update with::

   mamba update wakhan

To create a new environment, run:

mamba create --name myenvname wakhan

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/wakhan:<tag>

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

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