:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'hla-asm' .. highlight: bash hla-asm ======= .. conda:recipe:: hla-asm :replaces_section_title: :noindex: 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: :biotools:`hla-asm` .. conda:package:: hla-asm |downloads_hla-asm| |docker_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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `hla-asm/tags`_ for valid values for ````) .. |downloads_hla-asm| image:: https://img.shields.io/conda/dn/bioconda/hla-asm.svg?style=flat :target: https://anaconda.org/bioconda/hla-asm :alt: (downloads) .. |docker_hla-asm| image:: https://quay.io/repository/biocontainers/hla-asm/status :target: https://quay.io/repository/biocontainers/hla-asm .. _`hla-asm/tags`: https://quay.io/repository/biocontainers/hla-asm?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hla-asm/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/hla-asm/README.html