:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'gargammel' .. highlight: bash gargammel ========= .. conda:recipe:: gargammel :replaces_section_title: :noindex: Tool for simulating ancient DNA datasets :homepage: https://github.com/grenaud/gargammel :license: GPL-3.0-only :recipe: /`gargammel `_/`meta.yaml `_ gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present\-day human contamination and microbial contamination. .. conda:package:: gargammel |downloads_gargammel| |docker_gargammel| :versions: ``1.1.2-6``,  ``1.1.2-5``,  ``1.1.2-4``,  ``1.1.2-3``,  ``1.1.2-2``,  ``1.1.2-1``,  ``1.1.2-0`` :depends art: :depends gsl: ``>=2.7,<2.8.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends openssl: ``1.0.2n.*`` :depends perl: :depends samtools: :depends zlib: :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 gargammel and update with:: mamba update gargammel To create a new environment, run:: mamba create --name myenvname gargammel 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/gargammel: (see `gargammel/tags`_ for valid values for ````) .. |downloads_gargammel| image:: https://img.shields.io/conda/dn/bioconda/gargammel.svg?style=flat :target: https://anaconda.org/bioconda/gargammel :alt: (downloads) .. |docker_gargammel| image:: https://quay.io/repository/biocontainers/gargammel/status :target: https://quay.io/repository/biocontainers/gargammel .. _`gargammel/tags`: https://quay.io/repository/biocontainers/gargammel?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/gargammel/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/gargammel/README.html