:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'uvp' .. highlight: bash uvp === .. conda:recipe:: uvp :replaces_section_title: :noindex: A Unified Variant Pipeline to identify variants and assign lineage from MTBC sequence data. :homepage: https://github.com/CPTR-ReSeqTB/UVP :license: MIT :recipe: /`uvp `_/`meta.yaml `_ .. conda:package:: uvp |downloads_uvp| |docker_uvp| :versions: ``2.7.0-0``,  ``2.6.0-0`` :depends bcftools: ``1.2.*`` :depends bedtools: ``2.17.0.*`` :depends bwa: ``0.7.12.*`` :depends fastqc: ``0.11.5.*`` :depends fqtools: ``2.0.*`` :depends gatk: ``3.6.*`` :depends kraken: ``0.10.5.*`` :depends openjdk: ``8.*`` :depends perl-vcftools-vcf: ``0.1.16.*`` :depends picard: ``1.141.*`` :depends pigz: ``2.3.4.*`` :depends prinseq: ``0.20.4.*`` :depends python: :depends pyyaml: ``5.1.*`` :depends qualimap: ``2.1.3.*`` :depends samtools: ``1.2.*`` :depends snpeff: ``4.1.*`` :depends vcftools: ``0.1.16.*`` :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 uvp and update with:: mamba update uvp To create a new environment, run:: mamba create --name myenvname uvp 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/uvp: (see `uvp/tags`_ for valid values for ````) .. |downloads_uvp| image:: https://img.shields.io/conda/dn/bioconda/uvp.svg?style=flat :target: https://anaconda.org/bioconda/uvp :alt: (downloads) .. |docker_uvp| image:: https://quay.io/repository/biocontainers/uvp/status :target: https://quay.io/repository/biocontainers/uvp .. _`uvp/tags`: https://quay.io/repository/biocontainers/uvp?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/uvp/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/uvp/README.html