recipe haploflow

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++.

package haploflow

(downloads) docker_haploflow

versions:

1.0-5,  1.0-4,  1.0-3,  1.0-2,  1.0-1,  1.0-0,  0.1-1,  0.1-0

depends boost-cpp:

depends libgcc:

>=13

depends libstdcxx:

>=13

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `haploflow/tags`_ for valid values for ``<tag>``)

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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)