:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'haystac' .. highlight: bash haystac ======= .. conda:recipe:: haystac :replaces_section_title: :noindex: Species identification pipeline for both single species and metagenomic samples. :homepage: https://github.com/antonisdim/haystac :documentation: https://haystac.readthedocs.io/en/master/ :license: MIT / MIT :recipe: /`haystac `_/`meta.yaml `_ .. conda:package:: haystac |downloads_haystac| |docker_haystac| :versions: ``0.4.10-0``,  ``0.4.9-0``,  ``0.4.8-0``,  ``0.4.7-0``,  ``0.4-0``,  ``0.3.2-0``,  ``0.3.1-0``,  ``0.3-0``,  ``0.2-0`` :depends argparse: ``1.4.0.*`` :depends numpy: ``1.19.2.*`` :depends pandas: ``1.0.3.*`` :depends psutil: ``5.7.2.*`` :depends python: ``3.6.7.*`` :depends pyyaml: ``5.4.1.*`` :depends requests: ``2.24.0.*`` :depends snakemake-minimal: ``6.3.0.*`` :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 haystac and update with:: mamba update haystac To create a new environment, run:: mamba create --name myenvname haystac 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/haystac: (see `haystac/tags`_ for valid values for ````) .. |downloads_haystac| image:: https://img.shields.io/conda/dn/bioconda/haystac.svg?style=flat :target: https://anaconda.org/bioconda/haystac :alt: (downloads) .. |docker_haystac| image:: https://quay.io/repository/biocontainers/haystac/status :target: https://quay.io/repository/biocontainers/haystac .. _`haystac/tags`: https://quay.io/repository/biocontainers/haystac?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/haystac/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/haystac/README.html