:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'lorikeet-genome' .. highlight: bash lorikeet-genome =============== .. conda:recipe:: lorikeet-genome :replaces_section_title: :noindex: Metagenomic Variant Calling \& Diversity Analysis :homepage: https://github.com/rhysnewell/Lorikeet :documentation: https://rhysnewell.github.io/Lorikeet/ :license: GPL3 :recipe: /`lorikeet-genome `_/`meta.yaml `_ Lorikeet aims to call variants in metagenomes using local reassembly of haplotypes. .. conda:package:: lorikeet-genome |downloads_lorikeet-genome| |docker_lorikeet-genome| :versions: .. raw:: html
0.8.2-00.7.3-10.7.3-00.7.2-10.7.2-00.7.1-00.7.0-00.6.6-00.5.0-0 ``0.8.2-0``,  ``0.7.3-1``,  ``0.7.3-0``,  ``0.7.2-1``,  ``0.7.2-0``,  ``0.7.1-0``,  ``0.7.0-0``,  ``0.6.6-0``,  ``0.5.0-0``,  ``0.4.0-0``,  ``0.3.7-1``,  ``0.3.7-0``,  ``0.3.6-1``,  ``0.3.6-0``,  ``0.3.5-0``,  ``0.3.4-0``,  ``0.3.2-0`` .. raw:: html
:depends bcftools: :depends bwa: ``>=0.7.17`` :depends bwa-mem2: :depends cmake: ``>=3.21`` :depends coreutils: :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends minimap2: ``>=2.24`` :depends numpy: :depends openssl: ``>=3.2.0,<4.0a0`` :depends pip: :depends polars: ``>=0.18`` :depends prodigal: :depends python: ``3.10`` :depends samtools: ``>=1.9`` :depends scikit-allel: ``>=1.3.6`` :depends scipy: ``>=1.11`` :depends svim: :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 lorikeet-genome and update with:: mamba update lorikeet-genome To create a new environment, run:: mamba create --name myenvname lorikeet-genome 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/lorikeet-genome: (see `lorikeet-genome/tags`_ for valid values for ````) .. |downloads_lorikeet-genome| image:: https://img.shields.io/conda/dn/bioconda/lorikeet-genome.svg?style=flat :target: https://anaconda.org/bioconda/lorikeet-genome :alt: (downloads) .. |docker_lorikeet-genome| image:: https://quay.io/repository/biocontainers/lorikeet-genome/status :target: https://quay.io/repository/biocontainers/lorikeet-genome .. _`lorikeet-genome/tags`: https://quay.io/repository/biocontainers/lorikeet-genome?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/lorikeet-genome/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/lorikeet-genome/README.html