:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'sequana' .. highlight: bash sequana ======= .. conda:recipe:: sequana :replaces_section_title: :noindex: A set of standalone application and snakemake pipelines dedicated to NGS \(new generation sequencing\) analysis :homepage: http://sequana.readthedocs.io/ :documentation: https://sequana.readthedocs.io :developer docs: https://github.com/sequana/sequana :license: BSD / BSD-3-Clause :recipe: /`sequana `_/`meta.yaml `_ .. conda:package:: sequana |downloads_sequana| |docker_sequana| :versions: .. raw:: html
0.16.4-00.16.3-00.16.1-00.15.4-00.15.3-00.15.2-00.15.1-00.14.3-00.14.2-0 ``0.16.4-0``,  ``0.16.3-0``,  ``0.16.1-0``,  ``0.15.4-0``,  ``0.15.3-0``,  ``0.15.2-0``,  ``0.15.1-0``,  ``0.14.3-0``,  ``0.14.2-0``,  ``0.14.1-0``,  ``0.14.0-0``,  ``0.13.2-0``,  ``0.8.2-2``,  ``0.8.2-1``,  ``0.8.2-0``,  ``0.7.1-2``,  ``0.7.1-1``,  ``0.7.0-0``,  ``0.6.3.post1-0``,  ``0.6.1-0``,  ``0.6.0-0``,  ``0.5.2-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.1-0``,  ``0.4.0-0``,  ``0.3.0-0``,  ``0.2.1-0``,  ``0.2.0-0`` .. raw:: html
:depends adjusttext: :depends bioservices: ``>=1.10.0`` :depends brokenaxes: :depends bx-python: :depends click: ``>=8.1.0`` :depends colorlog: ``>=3.1.0`` :depends colormap: :depends cookiecutter: ``<2`` :depends cython: :depends deprecated: :depends docutils: :depends easydev: ``>=0.11.1`` :depends gseapy: :depends itolapi: :depends lxml: :depends matplotlib-base: ``<3.6`` :depends matplotlib-venn: :depends mock: :depends multiqc: ``<=1.11`` :depends packaging: :depends pandas: ``>=0.22`` :depends plotly: :depends psutil: :depends pykwalify: :depends pysam: ``>=0.16`` :depends python: ``>=3.8`` :depends rich-click: :depends ruamel.yaml: ``>=0.16.0`` :depends scikit-learn: :depends scipy: :depends seaborn: :depends selenium: :depends snakemake-minimal: ``>=7.16`` :depends statsmodels: :depends tqdm: :depends upsetplot: :depends vcfpy: :depends xlrd: :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 sequana and update with:: mamba update sequana To create a new environment, run:: mamba create --name myenvname sequana 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/sequana: (see `sequana/tags`_ for valid values for ````) .. |downloads_sequana| image:: https://img.shields.io/conda/dn/bioconda/sequana.svg?style=flat :target: https://anaconda.org/bioconda/sequana :alt: (downloads) .. |docker_sequana| image:: https://quay.io/repository/biocontainers/sequana/status :target: https://quay.io/repository/biocontainers/sequana .. _`sequana/tags`: https://quay.io/repository/biocontainers/sequana?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/sequana/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/sequana/README.html