recipe hla-asm

find HLA gene exon coordinates in long read-based assemblies and carry out HLA typing at G group resolution

Homepage:

https://github.com/DiltheyLab/HLA-LA/blob/master/HLA-ASM.md

License:

GPL

Recipe:

/hla-asm/meta.yaml

Links:

biotools: hla-asm

package hla-asm

versions:

1.0.1-0

depends bwa:

depends mummer:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bio-db-hts:

depends perl-bioperl:

depends perl-list-moreutils:

depends perl-text-levenshteinxs:

depends samtools:

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 hla-asm

and update with::

   mamba update hla-asm

To create a new environment, run:

mamba create --name myenvname hla-asm

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/hla-asm:<tag>

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

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