recipe arcas-hla

high-resolution HLA typing from RNA seq

Homepage:

https://github.com/RabadanLab/arcasHLA

License:

GPL-3.0-only

Recipe:

/arcas-hla/meta.yaml

Links:

doi: 10.1093/bioinformatics/btz474

arcasHLA performs high-resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.

package arcas-hla

(downloads) docker_arcas-hla

versions:
0.6.0-2,  0.6.0-1,  0.6.0-0,  0.5.0-3,  0.5.0-2,  0.5.0-1,  0.5.0-0,  0.4.0-0,  0.3.0-0, 

0.6.0-2,  0.6.0-1,  0.6.0-0,  0.5.0-3,  0.5.0-2,  0.5.0-1,  0.5.0-0,  0.4.0-0,  0.3.0-0,  0.2.5-0,  0.2.0-1,  0.2.0-0

depends bedtools:

depends biopython:

depends coreutils:

depends git:

depends git-lfs:

depends kallisto:

0.44

depends numpy:

depends pandas:

depends pigz:

depends pip:

depends pyarrow:

depends pytest:

depends python:

depends samtools:

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 arcas-hla

and update with::

   mamba update arcas-hla

To create a new environment, run:

mamba create --name myenvname arcas-hla

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/arcas-hla:<tag>

(see `arcas-hla/tags`_ for valid values for ``<tag>``)

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

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