recipe haproh

Identify runs of homozygosity (hapROH) and contamination (hapCon) in low coverage ancient human DNA data (1240K SNPs) using modern reference panel

Homepage:

https://github.com/hringbauer/hapROH

License:

GPL-3.0

Recipe:

/haproh/meta.yaml

package haproh

versions:

0.64-2,  0.64-1,  0.64-0,  0.63-0,  0.62-0,  0.61-0,  0.60-0,  0.53-0

depends cython:

depends h5py:

depends libgcc-ng:

>=12

depends matplotlib-base:

depends numdifftools:

depends numpy:

depends pandas:

depends psutil:

depends pysam:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends scipy:

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 haproh

and update with::

   mamba update haproh

To create a new environment, run:

mamba create --name myenvname haproh

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/haproh:<tag>

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

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