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SARA-Coffee is a structure based multiple RNA aligner.

This is a new algorithm that joins the pairwise RNA structure alignments performed by SARA with the multiple sequence T-Coffee framework.

SARA-Coffee VM

Since setting up the SARA-Coffee dependencies can be tricky we provide a self-contained Vagrant VM, which downloads and configures all the required pieces of software for you.

Install or update virtual box from

Install or update vagrant from:

Clone the sara-coffee virtual machine (this project) in a convenient location

$ git clone

Enter the sara-coffee-vm folder and launch vagrant:

$ cd sara-coffee-vm/
$  vagrant up  

The first time you run it, it will automatically download the virtual machine and all the packages required by SARA-Coffee. It may take some minutes to complete, so be patient.

When it boots up and the configuration steps are terminated, login into the VM instance:

$ vagrant ssh 

You are now in the Sara-Coffee virtual machine. Now you can run SARA-Coffee as shown:

$ cd sara_coffee_package/
$ ./ <input file> <output file> 

The folder '/vagrant/' is shared between the Sara-Coffee virtual and your local machine. On your local machine, this fiolder is the one in which you started vagrant (i.e. sara-coffee-vm)

When finished, stop the VM using the command vagrant halt or vagrant destroy, depending if you want to temporary stop the execution or delete permanently the VM with all its files.

Docker image

SARA-Coffee is also distributed as a Docker container. This will allow you to run it without having to install and configure each single dependency packages.

If you have Docker installed simply pull the SARA-Coffee container by using the command:

docker pull cbcrg/saracoffee

To run SARA-Coffee use the following command line:

docker run -v $PWD:$PWD -w $PWD cbcrg/saracoffee <input> <output>

Note: this command assumes your input file is located in the working directory. If this is not the case, you will need to mount the input file path accordingly.




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