:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'harvest-variants' .. highlight: bash harvest-variants ================ .. conda:recipe:: harvest-variants :replaces_section_title: :noindex: Harvest Variants is a pipeline for variant calling on SARS\-CoV\-2 samples :homepage: https://gitlab.com/treangenlab/sars-cov-2-harvest-variants :license: MIT :recipe: /`harvest-variants `_/`meta.yaml `_ .. conda:package:: harvest-variants |downloads_harvest-variants| |docker_harvest-variants| :versions: ``1.1.0-0``,  ``1.0.1-0``,  ``1.0.0-0``,  ``0.3.1-2``,  ``0.3.1-0``,  ``0.0.4-0``,  ``0.0.3-0`` :depends bcftools: ``>=1.15`` :depends bedtools: ``>=2.30.0`` :depends biopython: ``>=1.79`` :depends bwa: ``>=0.7.17`` :depends fastp: ``>=0.22`` :depends fastqc: ``>=0.11.9`` :depends lofreq: ``>=2.1.3`` :depends parsnp: ``>=1.7.4`` :depends python: ``>=3.6`` :depends pyvcf: ``>=0.6.8`` :depends samtools: ``>=1.15`` :depends snpeff: ``>=5.1`` :depends sra-tools: ``2.10.9.*`` :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 harvest-variants and update with:: mamba update harvest-variants To create a new environment, run:: mamba create --name myenvname harvest-variants 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/harvest-variants: (see `harvest-variants/tags`_ for valid values for ````) .. |downloads_harvest-variants| image:: https://img.shields.io/conda/dn/bioconda/harvest-variants.svg?style=flat :target: https://anaconda.org/bioconda/harvest-variants :alt: (downloads) .. |docker_harvest-variants| image:: https://quay.io/repository/biocontainers/harvest-variants/status :target: https://quay.io/repository/biocontainers/harvest-variants .. _`harvest-variants/tags`: https://quay.io/repository/biocontainers/harvest-variants?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/harvest-variants/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/harvest-variants/README.html