recipe saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Homepage:

https://github.com/sanger-pathogens/saffrontree

License:

GNU General Public License v3 (GPLv3)

Recipe:

/saffrontree/meta.yaml

Links:

doi: 10.21105/joss.00243

package saffrontree

(downloads) docker_saffrontree

versions:

0.1.2-0

depends biopython:

depends dendropy:

>=4.1.0

depends kmc:

>=2.3.0

depends libgcc:

depends pyfastaq:

>=3.12.0

depends python:

3.5*

requirements:

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 saffrontree

and update with::

   mamba update saffrontree

To create a new environment, run:

mamba create --name myenvname saffrontree

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/saffrontree:<tag>

(see `saffrontree/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/saffrontree/README.html)