recipe hla-la

HLA typing from short and long reads

Homepage:

https://github.com/DiltheyLab/HLA-LA

License:

GPL

Recipe:

/hla-la/meta.yaml

Links:

biotools: hla-la

package hla-la

versions:

1.0.4-0,  1.0.3-2,  1.0.3-1,  1.0.3-0,  1.0.1-6,  1.0.1-5,  1.0.1-4,  1.0.1-3,  1.0-2, 

1.0.4-0,  1.0.3-2,  1.0.3-1,  1.0.3-0,  1.0.1-6,  1.0.1-5,  1.0.1-4,  1.0.1-3,  1.0-2,  1.0-1,  1.0-0

depends bamtools:

2.5.1

depends boost-cpp:

1.74.00

depends bwa:

0.7.12

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends mummer:

depends perl-bio-db-hts:

>=3.1,<4.0a0

depends perl-bio-featureio:

depends perl-bioperl:

depends perl-bioperl-core:

1.7.8.*

depends perl-list-moreutils:

depends perl-text-levenshtein:

depends picard:

depends r-base:

4.*

depends samtools:

>=1.10

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-la

and update with::

   mamba update hla-la

To create a new environment, run:

mamba create --name myenvname hla-la

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-la:<tag>

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

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