recipe optitype

Precision HLA typing from next-generation sequencing data

Homepage:

https://github.com/FRED-2/OptiType

License:

BSD

Recipe:

/optitype/meta.yaml

package optitype

versions:

1.3.5-2,  1.3.5-1,  1.3.5-0,  1.3.4-0,  1.3.2-3,  1.3.2-2,  1.3.2-1,  1.3.1-0,  1.2.1-1, 

1.3.5-2,  1.3.5-1,  1.3.5-0,  1.3.4-0,  1.3.2-3,  1.3.2-2,  1.3.2-1,  1.3.1-0,  1.2.1-1,  1.2.1-0,  1.2-0

depends future:

depends glpk:

depends hdf5:

depends matplotlib-base:

depends numpy:

depends pandas:

depends pyomo:

depends pysam:

depends pytables:

depends python:

depends razers3:

depends samtools:

depends six:

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 optitype

and update with::

   mamba update optitype

To create a new environment, run:

mamba create --name myenvname optitype

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/optitype:<tag>

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

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Link to this page

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