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_sources/recipes/corona_lineage_dynamics/README.rst.txt
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| :orphan: .. only available via index, not via toctree | ||
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| .. title:: Package Recipe 'corona_lineage_dynamics' | ||
| .. highlight: bash | ||
| corona_lineage_dynamics | ||
| ======================= | ||
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| .. conda:recipe:: corona_lineage_dynamics | ||
| :replaces_section_title: | ||
| :noindex: | ||
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| Analyzing and visualizing pangolin lineages of GISAID metadata. | ||
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| :homepage: https://github.com/hzi-bifo/corona_lineage_dynamics | ||
| :license: OTHER / ASL | ||
| :recipe: /`corona_lineage_dynamics <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/corona_lineage_dynamics>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/corona_lineage_dynamics/meta.yaml>`_ | ||
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| .. conda:package:: corona_lineage_dynamics | ||
| |downloads_corona_lineage_dynamics| |docker_corona_lineage_dynamics| | ||
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| :versions: | ||
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| ``0.1.5-0`` | ||
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| :depends boost: | ||
| :depends libboost: ``>=1.84.0,<1.85.0a0`` | ||
| :depends libgcc: ``>=13`` | ||
| :depends libstdcxx: ``>=13`` | ||
| :depends libzlib: ``>=1.3.1,<2.0a0`` | ||
| :depends r-base: ``>=4.4,<4.5.0a0`` | ||
| :depends r-binom: | ||
| :depends r-countrycode: | ||
| :depends r-d3heatmap: | ||
| :depends r-devtools: | ||
| :depends r-doparallel: | ||
| :depends r-dplyr: | ||
| :depends r-foreach: | ||
| :depends r-htmltools: | ||
| :depends r-htmlwidgets: | ||
| :depends r-knitr: | ||
| :depends r-lifecycle: | ||
| :depends r-mass: | ||
| :depends r-matrix: | ||
| :depends r-pkgdown: | ||
| :depends r-plotly: | ||
| :depends r-plyr: | ||
| :depends r-ragg: | ||
| :depends r-rcpp: | ||
| :depends r-rcurl: | ||
| :depends r-readr: | ||
| :depends r-scales: | ||
| :depends r-stringr: | ||
| :depends r-systemfonts: | ||
| :depends r-tictoc: | ||
| :depends r-tidyr: | ||
| :depends r-withr: | ||
| :depends r-xml2: | ||
| :depends r-xtable: | ||
| :depends ta-lib: | ||
| :depends zlib: | ||
| :requirements: | ||
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| :additional platforms: | ||
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| .. rubric:: Installation | ||
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| You need a conda-compatible package manager | ||
| (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_) | ||
| and the Bioconda channel already activated (see :ref:`set-up-channels`). | ||
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| While any of above package managers is fine, it is currently recommended to use either | ||
| micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions). | ||
| We will show all commands using mamba below, but the arguments are the same for the two | ||
| others. | ||
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| Given that you already have a conda environment in which you want to have this package, install with:: | ||
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| mamba install corona_lineage_dynamics | ||
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| and update with:: | ||
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| mamba update corona_lineage_dynamics | ||
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| To create a new environment, run:: | ||
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| mamba create --name myenvname corona_lineage_dynamics | ||
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| with ``myenvname`` being a reasonable name for the environment | ||
| (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options). | ||
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| Alternatively, use the docker container:: | ||
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| docker pull quay.io/biocontainers/corona_lineage_dynamics:<tag> | ||
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| (see `corona_lineage_dynamics/tags`_ for valid values for ``<tag>``) | ||
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| .. |downloads_corona_lineage_dynamics| image:: https://img.shields.io/conda/dn/bioconda/corona_lineage_dynamics.svg?style=flat | ||
| :target: https://anaconda.org/bioconda/corona_lineage_dynamics | ||
| :alt: (downloads) | ||
| .. |docker_corona_lineage_dynamics| image:: https://quay.io/repository/biocontainers/corona_lineage_dynamics/status | ||
| :target: https://quay.io/repository/biocontainers/corona_lineage_dynamics | ||
| .. _`corona_lineage_dynamics/tags`: https://quay.io/repository/biocontainers/corona_lineage_dynamics?tab=tags | ||
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| .. raw:: html | ||
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| <script> | ||
| var package = "corona_lineage_dynamics"; | ||
| var versions = ["0.1.5"]; | ||
| </script> | ||
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| Download stats | ||
| ----------------- | ||
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| .. raw:: html | ||
| :file: ../../templates/package_dashboard.html | ||
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| Link to this page | ||
| ----------------- | ||
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| Render an |install-with-bioconda| badge with the following MarkDown:: | ||
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| [](http://bioconda.github.io/recipes/corona_lineage_dynamics/README.html) | ||
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| .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat | ||
| :target: http://bioconda.github.io/recipes/corona_lineage_dynamics/README.html |
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