recipe orthanq

Uncertainty aware HLA typing and general haplotype quantification

Homepage:

https://github.com/orthanq/orthanq

License:

MIT / MIT

Recipe:

/orthanq/meta.yaml

package orthanq

(downloads) docker_orthanq

versions:
1.7.9-0,  1.7.8-0,  1.7.7-0,  1.7.6-0,  1.7.5-0,  1.7.4-0,  1.7.2-0,  1.7.1-0,  1.7.0-2, 

1.7.9-0,  1.7.8-0,  1.7.7-0,  1.7.6-0,  1.7.5-0,  1.7.4-0,  1.7.2-0,  1.7.1-0,  1.7.0-2,  1.7.0-1,  1.7.0-0,  1.6.0-0,  1.5.0-1,  1.5.0-0,  1.4.0-1,  1.4.0-0,  1.3.2-0,  1.3.0-0,  1.2.0-0,  1.1.0-0

depends bwa:

>=0.7.18,<0.8.0a0

depends bzip2:

>=1.0.8,<2.0a0

depends clangdev:

depends coin-or-cbc:

>=2.10.12,<2.11.0a0

depends coincbc:

depends fontconfig:

>=2.14.2,<3.0a0

depends fonts-conda-ecosystem:

depends gsl:

>=2.7,<2.8.0a0

depends hdf5:

1.10.5.*

depends hdf5:

>=1.10.5,<1.10.6.0a0

depends htslib:

>=1.21,<1.22.0a0

depends libcblas:

>=3.9.0,<4.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends minimap2:

>=2.28,<3.0a0

depends openssl:

>=3.3.2,<4.0a0

depends samtools:

>=1.19.2,<2.0a0

depends varlociraptor:

>=8.4.7,<9.0a0

depends vg:

>=1.56.0,<2.0a0

depends xz:

>=5.2.6,<6.0a0

depends zlib:

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 orthanq

and update with::

   mamba update orthanq

To create a new environment, run:

mamba create --name myenvname orthanq

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/orthanq:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/orthanq/README.html)