recipe rappas

RAPPAS (Rapid Alignment-free Phylogenetic PLacement via Ancestral Sequences) is a program dedicated to Phylogenetic Placement of (meta)genomic reads on a reference tree. As apposed to previous PP programs, RAPPAS is based on the phylo-kmers idea, detailed in tis manuscript and uses a 2 step approach divided into a) the database build, and b) the placement itself. The main advantage of RAPPAS is that it is alignment free, which means that after step (a) (the DB build) is performed, metagenomic reads can be directly placed on a referene tree WITHOUT aligning them to the reference alignment on which the tree was built (as required by other approaches). The second advantage of RAPPAS is its algorithm based on phylo-kmers matches, making its execution time linear with respect to the length of the placed sequences.

Homepage:

https://github.com/blinard-BIOINFO/RAPPAS

License:

GPL3

Recipe:

/rappas/meta.yaml

package rappas

(downloads) docker_rappas

versions:

1.22-0,  1.21-0,  1.20-0,  1.12-0

depends font-ttf-dejavu-sans-mono:

depends openjdk:

>=8.0.144

depends phyml:

3.3.20190909.*

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 rappas

and update with::

   mamba update rappas

To create a new environment, run:

mamba create --name myenvname rappas

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/rappas:<tag>

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