![cmv](http://www.bioinf.uni-freiburg.de/~egg/cmvlogo.png "cmv") 
=========
*cmv* is a collection of tools for the visualisation of Hidden Markov Models (*HMMV*) and RNA-family models (*CMV*).
Moreover it can visualise comparisons of these models (*HMMCV*,*CMCV*), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure.

They are available as a commandline tools and as a webservice [cmvs](http://rna.informatik.uni-freiburg.de/CMVS/).

The source code of *cmv* is open source and available via GitHub and Hackage (License GPL-3):

*   [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) [![Docker Repository on Quay](https://quay.io/repository/biocontainers/cmv/status "Docker Repository on Quay")](https://quay.io/repository/repository/biocontainers/cmv)

For instruction how to use *cmv* please see the [Help page.](http://www.gapjunction.eu/cmvs/help)

## Installation
For Linux we recommend installation via bioconda, for macOS usage of the docker container.
The example input files used in the webservice (EGF, Piwi, Hammerhead Clan, tRNA Clan) can be retrieved here: [Example input](http://www.gapjunction.eu/data/cmvs/exampleInput.zip)

### Installation via bioconda - Linux

*cmv* can be installed with all dependencies via [conda](https://conda.io/docs/install/quick.html). Once you have conda installed simply type:

       conda install -c bioconda -c conda-forge cmv
       
### Usage via biocontainer docker - MacOS

*cmv* can be retrieved and used as docker container with all dependencies via [docker](https://docs.docker.com/engine/installation/). Once you have docker installed simply type:

       docker run -i -t quay.io/biocontainers/cmv:1.0.7--0 /bin/bash

### Installation via cabal-install

cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem [cabal](https://www.haskell.org/cabal/). CMV is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Additionally to cabal you require [cairo](https://cairographics.org/), [pango](http://www.pango.org/), [happy](https://www.haskell.org/happy/) and [alex](https://www.haskell.org/alex/) which can be installed via the distribution package manager e.g. Ubuntu: 
        
        sudo apt-get install libcairo2 libpango1.0-0 libpangomm-1.4-dev happy alex
   
Once you have cabal installed simply type:

         cabal install cmv

### Optional Dependencies:
*cmv* creates output which can be visualised via following optional dependencies.
* [R2R](http://breaker.research.yale.edu/R2R/)
* [forna](http://rna.tbi.univie.ac.at/forna/)

### Precompiled Executables

* Linux (ghc-8.2.2) [HMMV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV)
* Linux (ghc-8.2.2) [HMMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV)
* Linux (ghc-8.2.2) [CMV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV)
* Linux (ghc-8.2.2) [CMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV)
* Linux (ghc-8.2.2) [CMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCWStoCMCV)