:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'fastspar' .. highlight: bash fastspar ======== .. conda:recipe:: fastspar :replaces_section_title: :noindex: Rapid and scalable correlation estimation for compositional data :homepage: https://github.com/scwatts/fastspar :license: GPLv3 :recipe: /`fastspar `_/`meta.yaml `_ :links: doi: :doi:`10.1093/bioinformatics/bty734`, doi: :doi:`10.1371/journal.pcbi.1002687` FastSpar is a C\+\+ implementation of the SparCC algorithm which is up to several thousand times faster than the original Python2 release and uses much less memory. The FastSpar implementation provides threading support and a p\-value estimator which accounts for the possibility of repetitious data permutations. .. conda:package:: fastspar |downloads_fastspar| |docker_fastspar| :versions: ``1.0.0-5``,  ``1.0.0-4``,  ``1.0.0-3``,  ``1.0.0-2``,  ``1.0.0-1``,  ``1.0.0-0``,  ``0.0.10-0``,  ``0.0.9-0``,  ``0.0.6-0`` :depends armadillo: ``>=12.2,<13.0a0`` :depends armadillo: ``>=7.800.1`` :depends gsl: ``>=2.7,<2.8.0a0`` :depends libgcc-ng: ``>=12`` :depends libgfortran-ng: :depends libgfortran5: ``>=12.2.0`` :depends libstdcxx-ng: ``>=12`` :depends openblas: ``* *openmp*`` :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 fastspar and update with:: mamba update fastspar To create a new environment, run:: mamba create --name myenvname fastspar 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/fastspar: (see `fastspar/tags`_ for valid values for ````) .. |downloads_fastspar| image:: https://img.shields.io/conda/dn/bioconda/fastspar.svg?style=flat :target: https://anaconda.org/bioconda/fastspar :alt: (downloads) .. |docker_fastspar| image:: https://quay.io/repository/biocontainers/fastspar/status :target: https://quay.io/repository/biocontainers/fastspar .. _`fastspar/tags`: https://quay.io/repository/biocontainers/fastspar?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/fastspar/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/fastspar/README.html