Presumably you are reading this file on our github site and thus you are likely to know that the following commands on your local machine should get you going:
git clone https://github.com/BrendelGroup/MoVRs
cd MoVRs/That said, an implicit assumption is that your local machine runs some version of Linux. For genome-wide DNA motif finding you will likely work with large date sets. The open (source) MoVRs software will make the analysis of these data sets easy, accurate, meaningful, reproducible, and scalable (our RAMOSE philosophy and promise). The output of MoVRs will be nicely organized but intermediate output files will be kept initially, so you will need sufficient disk space. It will be up to you to specify the number of processors to be used in various parallel steps during the workflow. We like to have 4-10 processors dedicated to the task (although most of the time, fewer processors will be used). Even then, be prepared to wait a few hours until all is done. Sounds bad? Not really, because the whole analysis is quite a complex process, but both the original setup of MoVRs and the setup of particular analyses takes only a few minutes each. Once launched, go on thinking about your science, or start drafting the paper!
MoVRs is a workflow that invokes easily available third-party software as well as scripts developed in our group. As a first step, go to the src directory and install required programs as per instructions in the README file in that directory. You will need to keep track of the paths to the installed binaries. Although quite a few external programs are involved, typical installation can be scripted (as described) and would not take more than a few minutes.
MoVRs relies on a number of bash, Perl, python, and R scripts that are placed in the scripts directory. The Perl, python, and R scripts use various packages that must be pre-installed on your system. Run the xcheckprerequisites bash script in the scripts directory to see what is available. If packages are missing, you need to install them prior to running the MoVRs workflow (there are different ways to install these packages; if in doubt, ask your systems administrator).
proceed to the HOWTO document, and we'll tell you how to execute sample workflows (or, equally easy, your very own data analyses).