:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'stacks' .. highlight: bash stacks ====== .. conda:recipe:: stacks :replaces_section_title: :noindex: Stacks is a software pipeline for building loci from RAD\-seq :homepage: https://catchenlab.life.illinois.edu/stacks/ :license: GPL :recipe: /`stacks `_/`meta.yaml `_ :links: biotools: :biotools:`Stacks`, doi: :doi:`10.1111/mec.12354` .. conda:package:: stacks |downloads_stacks| |docker_stacks| :versions: .. raw:: html
2.65-02.64-02.61-12.61-02.60-12.60-02.55-12.55-02.53-1 ``2.65-0``,  ``2.64-0``,  ``2.61-1``,  ``2.61-0``,  ``2.60-1``,  ``2.60-0``,  ``2.55-1``,  ``2.55-0``,  ``2.53-1``,  ``2.53-0``,  ``2.52-0``,  ``2.5-0``,  ``2.4-1``,  ``2.4-0``,  ``2.3-6``,  ``2.3-5``,  ``2.3-4``,  ``2.3-3``,  ``2.3d-1``,  ``2.3d-0``,  ``2.3c-3``,  ``2.3c-2``,  ``2.3c-1``,  ``2.3c-0``,  ``2.3b-3``,  ``2.3b-2``,  ``2.3b-1``,  ``2.3b-0``,  ``2.2-6``,  ``2.2-5``,  ``2.2-4``,  ``2.2-3``,  ``2.2-2``,  ``2.2-1``,  ``2.2-0``,  ``2.1-5``,  ``2.1-4``,  ``2.1-3``,  ``2.1-2``,  ``2.1-1``,  ``2.0-4``,  ``2.0-3``,  ``2.0-2``,  ``2.0-1``,  ``2.0-0``,  ``2.0Beta10a-0``,  ``2.0Beta9-0``,  ``2.0Beta8-1``,  ``2.0Beta8-0``,  ``2.0Beta8c-1``,  ``2.0Beta8c-0``,  ``2.0Beta7c-0``,  ``1.48-1``,  ``1.48-0``,  ``1.47-2``,  ``1.47-1``,  ``1.47-0``,  ``1.46-4``,  ``1.46-3``,  ``1.46-2``,  ``1.46-1``,  ``1.46-0``,  ``1.44-3``,  ``1.44-2``,  ``1.44-1``,  ``1.44-0``,  ``1.43-2``,  ``1.43-1``,  ``1.43-0``,  ``1.42-5``,  ``1.42-4``,  ``1.42-3``,  ``1.42-2``,  ``1.42-1``,  ``1.40-3``,  ``1.40-2``,  ``1.40-1``,  ``1.40-0``,  ``1.37-5``,  ``1.37-4``,  ``1.37-3``,  ``1.37-2``,  ``1.37-1``,  ``1.37-0`` .. raw:: html
:depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends openmp: :depends perl: :depends perl-bioperl-core: :depends perl-file-spec: :depends perl-file-temp: :depends perl-posix: :depends python: ``>=3`` :depends r-base: ``>=4`` :depends samtools: :depends velvet: :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 stacks and update with:: mamba update stacks To create a new environment, run:: mamba create --name myenvname stacks 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/stacks: (see `stacks/tags`_ for valid values for ````) .. |downloads_stacks| image:: https://img.shields.io/conda/dn/bioconda/stacks.svg?style=flat :target: https://anaconda.org/bioconda/stacks :alt: (downloads) .. |docker_stacks| image:: https://quay.io/repository/biocontainers/stacks/status :target: https://quay.io/repository/biocontainers/stacks .. _`stacks/tags`: https://quay.io/repository/biocontainers/stacks?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/stacks/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/stacks/README.html