Methods for performing the pipeline using the Galaxy Download.

Here you will find information on setting up the downloadable RNAmapper Galaxy implementation. The underlying steps involved in mapping using Galaxy or the command line are the same. However, the Galaxy package, once setup, provides a much easier "point and click"  experience.

While Galaxy may be easier then the command line, there is still a learning curve. There are several good webcasts that will help as you get going.
    Galaxy help and screencasts
Additionally, you will need a powerful desktop machine to run the Galaxy implemention. The machine needs a minimum of 16GB of RAM, 250GB of free harddrive space, and must have a 64bit processor.
First download the latest version of RNAmapper on Galaxy. It is hosted on the Megason lab's website:
    Megason RNAmapper download
You will also find downloads for MEGAmapper, a software that uses whole genome sequencing to map and identify mutations as well as other useful goodies such as SNP datasets.

The RNAmapper download is a complete virtual machine containing Galaxy, RNAmapper, SNP databases, the zebrafish reference genome and indices, open-source programs, and sample RNA-Seq data. This is a very large download and will likely take >1 day to finish. Also, unzipping this file requires the use of either WinRAR (site) or Zipeg (site). You will also need to install VirtualBox (site).

RNAmapper documentation: source code, license


Go to and download the appropriate installer for your operating system. Install VirtualBox on your machine. After the necessary reboot, launch VirtualBox

Creating a new virtual machine
Create a new virtual machine and call it “galaxy”. Choose “Linux” as operating system and set the version to “Ubuntu (64bit)”. Note that you cannot “simulate” a 64bit architecture. Reminder: your processor must be 64bit capable to use RNAmapper. Click “next.”


Give your virtual machine some memory - the more, the better, but do not move the slider into the red zone. If you assign all of your host computers RAM to the virtual machine you will likely experience stability issues. You will need at least 8GB of RAM available to the virtual machine to operate Galaxy successfully. Click “next.”


You will need to download the current version of RNAmapper (see top) and unpack it. Now it is time to link to this virtual disk. Select “Use existing hard disk” and browse to the location of the unpacked data.vdi. Make sure that data.vdi is placed on a physical HDD with at least 250GB of free disk space - the more, the better. Then click “Next” and finish the dialogue.


Tuning virtual machine parameters
Once the virtual machine is created, begin the “Settings” dialogue from the main menu. In the “System” submenu on the “Motherboard” tab, make sure that you have more than 8 GB of base memory. Avoid moving the slider into the red zone, or your parent OS may no longer run stably. Adjust the boot order so that “Hard Disk” is at the top of the queue.


In the “Processor” tab, assign as many CPUs as your computer can handle. Again, avoid going into the red zone.


Finally, in the “Acceleration” tab, make sure that “Enable VT-x/AMD-V” is enabled. If this option is greyed out, you must enable VT-x support in your BIOS before you can proceed.


Now go to “Display” submenu and make sure that you have allocated some video memory. Also, enable “3D video acceleration.”


Now switch to the “Storage” submenu. Use the right disk stack icon (HDD) in the highlighted “SATA Controller” option to add your virtual disk. If data.vdi is already added to the SATA Controller section you can skip this and the next step.


This will bring up the disk dialogue. Proceed by choosing an existing disk. Choose “data.vdi” from the location where you put it.


You will want to move data between the virtual machine and your host system, so you must specify a shared folder between the two. Select the “Shared Folders” submenu. Then select the “add folder” icon in the top right corner.


Now browse to the location of the host machine folder you wish to share, and enable the “Auto-mount” option. Click “OK.” Once you launch the virtual machine, your shared folder will be under “/media/sf_virtualbox_shared”.


Congratulations! You can now start your virtual machine. Remember, the user account is "galaxy", the password is also "galaxy".

Once your virtual machine is launched you will be running a virtual linux based system that will have the many operating system tools available, including text editors, terminals, etc, which can be found on the left-hand bar. However, you can focus on the desktop links that will lead you to folders of interest and Firefox as these will be the tools of most use.

Now that you have a running RNAmapper its time to start mapping your mutants. -- Galaxy 101

If you encounter problems, have questions or suggestions, please email: RNAmapper at gmail dot com

GPL by Nikolaus Obholzer, 2012