- 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:
- License:
GPL3
- Recipe:
- package rappas¶
- Versions:
1.22-0,1.21-0,1.20-0,1.12-0- Depends:
on font-ttf-dejavu-sans-mono
on openjdk
>=8.0.144on phyml
3.3.20190909.*
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install rappas
to add into an existing workspace instead, run:
pixi add rappas
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install rappas
Alternatively, to install into a new environment, run:
conda create -n envname rappas
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/rappas:<tag>
(see rappas/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/rappas/README.html)
