===================================================
   Instructions on how to run Metagenome Orchestra
   (Orchestra or Mago for short) within an
   Oracle VirtualBox virtual machine.

   Orchestra homepage:
   http://mago.fe.uni-lj.si
===================================================





   ---------------------------
   DOWNLOADING ORCHESTRA IMAGE
   ---------------------------

1. Make sure that Oracle VirtualBox is installed on
   your system. Please refer to web page
   https://www.virtualbox.org/
   for VirtualBox information and installation files.





2. Download Orchestra virtual machine image:

   http://mago.fe.uni-lj.si/mago_V2_2_virtualbox.ova

   and save it in a local directory of your choice.





3.  Start Oracle VM VirtualBox Manager.

    In File menu, select Import Appliance.

    In the entry "Appliance to import" point to the
    downloaded Orchestra OVA file.

    Click "Import" and accept license
    agreement. The import process begins and it
    takes a while. If everything goes well,
    your Orchestra virtual machine is ready to run.

    Run it by selecting "Metagenome Orchestra"
    virtual machine in Oracle VM VirtualBox
    manager and clicking Start.

    Orchestra virtual machine does not require
    a password to login. For advanced tasks
    like installing of new packages or running
    sudo command, use:
    username: mago
    password: mago





   --------------------------
   RUNNING ORCHESTRA PIPELINE
   --------------------------

   To test Orchestra setup and to get the idea
   about how Orchestra works, we prepared a
   simple demo setup, which is included in the
   Orchestra virtual machine. Demo files
   are located in directory:

   /home/mago/mago_demo_V2_2/

   To run demo, double click desktop icon
   "Run Demo". This opens a terminal
   window in which Orchestra demo execution
   can be monitored. The resulting files
   start appearing in directory:

   /home/mago/mago_demo_V2_2_output/



   As an alternative way to run demo,
   open Linux terminal and execute:

   mago /home/mago/mago_demo_V2_2/demo_vbox.txt

   Orchestra starts processing.
   File demo_vbox.txt instructs Orchestra
   to output results of processing to directory:
   /home/mago/mago_demo_V2_2_output/



   For real metagenome analyses prepare your input
   reads in a directory of your preference, and
   constellate a suitable configuration file,
   based on a configuration template (which is
   also a user manual) at

   http://mago.fe.uni-lj.si/config_template_V2_2.txt