recipe orthanq

Uncertainty aware HLA typing and general haplotype quantification.

Homepage:

https://github.com/orthanq/orthanq

Documentation:

https://orthanq.github.io

License:

MIT / MIT

Recipe:

/orthanq/meta.yaml

package orthanq

versions:

1.16.1-0,  1.16.0-0,  1.15.0-0,  1.14.0-0,  1.13.0-0,  1.12.1-1,  1.12.1-0,  1.10.0-1,  1.10.0-0, 

1.16.1-0,  1.16.0-0,  1.15.0-0,  1.14.0-0,  1.13.0-0,  1.12.1-1,  1.12.1-0,  1.10.0-1,  1.10.0-0,  1.9.3-0,  1.9.2-0,  1.9.1-0,  1.9.0-0,  1.8.0-0,  1.7.9-1,  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:

depends bzip2:

>=1.0.8,<2.0a0

depends coin-or-cbc:

>=2.10.12,<2.11.0a0

depends fontconfig:

>=2.15.0,<3.0a0

depends fonts-conda-ecosystem:

depends gsl:

>=2.7,<2.8.0a0

depends htslib:

depends libcblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends minimap2:

depends openssl:

>=3.5.4,<4.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

1.20

depends varlociraptor:

8.7.3

depends vg:

1.63.1

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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>``)

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