:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'deepaclive' .. highlight: bash deepaclive ========== .. conda:recipe:: deepaclive :replaces_section_title: :noindex: Detecting novel pathogens from NGS reads in real\-time during a sequencing run. :homepage: https://gitlab.com/dacs-hpi/deepac-live :license: MIT / MIT :recipe: /`deepaclive `_/`meta.yaml `_ .. conda:package:: deepaclive |downloads_deepaclive| |docker_deepaclive| :versions: ``0.3.2-0``,  ``0.3.0-0``,  ``0.2.0-0``,  ``0.1.0-0`` :depends biopython: ``>=1.76`` :depends deepac: ``>=0.12.0`` :depends matplotlib-base: ``>=3.1.3`` :depends paramiko: ``>=2.7.1`` :depends pysam: ``>=0.15.4`` :depends python: ``>=3`` :depends samtools: ``>=1.9`` :depends scikit-learn: ``>=0.22.1`` :depends tensorflow: ``>=2.1`` :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 deepaclive and update with:: mamba update deepaclive To create a new environment, run:: mamba create --name myenvname deepaclive 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/deepaclive: (see `deepaclive/tags`_ for valid values for ````) .. |downloads_deepaclive| image:: https://img.shields.io/conda/dn/bioconda/deepaclive.svg?style=flat :target: https://anaconda.org/bioconda/deepaclive :alt: (downloads) .. |docker_deepaclive| image:: https://quay.io/repository/biocontainers/deepaclive/status :target: https://quay.io/repository/biocontainers/deepaclive .. _`deepaclive/tags`: https://quay.io/repository/biocontainers/deepaclive?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/deepaclive/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/deepaclive/README.html