recipe whatshap

phase genomic variants using DNA sequencing reads (haplotype assembly)

Homepage:

https://whatshap.readthedocs.io/

License:

MIT License

Recipe:

/whatshap/meta.yaml

Links:

biotools: whatshap, doi: 10.1089/cmb.2014.0157

package whatshap

(downloads) docker_whatshap

versions:
2.2-02.1-02.0-01.7-11.7-01.6-11.6-01.5-01.4-1

2.2-02.1-02.0-01.7-11.7-01.6-11.6-01.5-01.4-11.4-01.3-11.3-01.2.1-11.2.1-01.1-11.1-01.0-11.0-00.18-00.17-00.16-00.15-00.14.1-00.13-00.12-00.11-00.9-0

depends biopython:

>=1.73

depends htslib:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends networkx:

>=2.4

depends pulp:

>=2

depends pyfaidx:

>=0.5.5.2

depends pysam:

>=0.18

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends scipy:

depends xopen:

>=1.2.0

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 whatshap

and update with::

   mamba update whatshap

To create a new environment, run:

mamba create --name myenvname whatshap

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/whatshap:<tag>

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

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