cmv-1.0.6: README.md

![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.](192.52.2.124/cmvs/help)

### Usage via biocontainer (docker)

*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:1.0.5--0 /bin/bash

### Installation via bioconda

*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
       
### 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-8.0.2) [HMMV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV)
* Linux (ghc-8.0.2) [HMMCV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV)
* Linux (ghc-8.0.2) [CMV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV)
* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV)
* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCWStoCMCV)