recipe fastreer

Phylogenetic, distance, and tree-building utilities for VCF and FASTA files

Homepage:

https://github.com/gkanogiannis/fastreeR

License:

GPL / GPL-3.0-only

Recipe:

/fastreer/meta.yaml

Links:

doi: 10.1186/s12859-016-1186-3

fastreeR is a Python+Java CLI tool for calculating distance matrices from VCF or FASTA files and constructing Newick trees using a Java backend and Python frontend.

package fastreer

(downloads) docker_fastreer

versions:

1.13.23-0

depends openjdk:

>=8.0.144

depends python:

>=3.9

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 fastreer

and update with::

   mamba update fastreer

To create a new environment, run:

mamba create --name myenvname fastreer

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/fastreer:<tag>

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

Download stats

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/fastreer/README.html)