:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'haploflow' .. highlight: bash haploflow ========= .. conda:recipe:: haploflow :replaces_section_title: :noindex: Strain\-aware viral genome assembler for short read sequence data :homepage: https://github.com/hzi-bifo/Haploflow :license: Apache-2.0 AND MIT :recipe: /`haploflow `_/`meta.yaml `_ Haploflow is a strain\-aware viral genome assembler for short read sequence data. It uses a flow algorithm on a deBruijn graph data structure to resolve viral strains. Haploflow is still actively under development and written entirely in C\+\+. .. conda:package:: haploflow |downloads_haploflow| |docker_haploflow| :versions: ``1.0-3``,  ``1.0-2``,  ``1.0-1``,  ``1.0-0``,  ``0.1-1``,  ``0.1-0`` :depends boost-cpp: ``>=1.78.0,<1.78.1.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :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 haploflow and update with:: mamba update haploflow To create a new environment, run:: mamba create --name myenvname haploflow 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/haploflow: (see `haploflow/tags`_ for valid values for ````) .. |downloads_haploflow| image:: https://img.shields.io/conda/dn/bioconda/haploflow.svg?style=flat :target: https://anaconda.org/bioconda/haploflow :alt: (downloads) .. |docker_haploflow| image:: https://quay.io/repository/biocontainers/haploflow/status :target: https://quay.io/repository/biocontainers/haploflow .. _`haploflow/tags`: https://quay.io/repository/biocontainers/haploflow?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/haploflow/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/haploflow/README.html