- recipe rnaclust
A tool for clustering of RNAs based on their secondary structures using LocARNA
- Homepage:
http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/
- License:
GPL / GPL-2.0
- Recipe:
- Links:
biotools: RNAclust
RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file. In the first step for each input sequence the base pair probability matrix of its secondary structure distribution is calculated (using RNAfold from the Vienna RNA package). Secondly, for each pair of base pair probability matrices a sequence-structure alignment is calculated using LocARNA. Lastly, a hierarchical cluster-tree (in NEWICK format) is derived by WPGMA clustering of the pairwise alignment distances and the optimal number of clusters is calculated from the tree.
- package rnaclust¶
- Versions:
1.3-0- Depends:
on libgcc
on locarna
on perl
5.22.0*on viennarna
- 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 rnaclust
to add into an existing workspace instead, run:
pixi add rnaclust
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 rnaclust
Alternatively, to install into a new environment, run:
conda create -n envname rnaclust
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/rnaclust:<tag>
(see rnaclust/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/rnaclust/README.html)
