Scrimer virtual machine

The virtual machine is the easiest way to test Scrimer. You get a computer preinstalled with Scrimer, many of its dependencies and a test data set. The test data set is a complete scrimer run with all the intermediate files generated from a subset of reads from our nightingale data set, using zebra finch as a reference genome.

The machine is set up tu use 2 GB of RAM and one CPU. Those settings can be adjusted in the main VirtualBox interface. We decieded to use 32 bit machine, because it is the most compatible setting. The downside is that you cannot use more than 4 GB of RAM. We can provide 64 bit image on request.

Because of licensing issues, the image does not contain Newbler. Trinity is not included as well, because of high memory requirements of the assembly. We recommend to perform the assembly on a dedicated machine and then transfer the data back to the scrimer project directory.

Virtual machine installation

Installation steps (it should take less than 10 minutes):

  • Install VirtualBox ( It works on Windows, Linux and Mac.
  • Download the virtual machine image from You’ll get a single file with .ova extension on your hard drive.
  • You can either double click the .ova file, or run VirtualBox, and choose File > Import Appliance. Follow the instructions after the import is started.

After a successful instalation you should see something like this (only the machine list will contain jsut one machine). Check whether you can start the virtual machine: click Start in the main VirtualBox window:


After a while you should see something like this:


You don’t need to type anything into that window, just checking that it looks like the screenshot is enough.

Machine configuration details:

  • Administrative user: root, password: debian
  • Normal user: user, password: user
  • ssh on port 2222


Install PuTTY and WinSCP. PuTTY will be used to control the virtual computer. WinSCP will be used to transfer files between your computer and the virtual computer.

Mac OS X and Linux

Ssh is used to control the virtual computer. It should be installed in your computer.

Files can be transferred with scp, rsync or lftp (recommended) from the command line. Scp and rsync could be already installed in your system, if you want to use lftp, you’ll probably have to install it yourself.

Mac users that prefer grapical clients can use something like CyberDuck. See .

Connecting to the virtual machine


You need to start the virtual machine first!

Connect to control the machine

To control the machine, you need to connect to the ssh service.

In Windows this is done with PuTTY.

  • start PuTTY
  • fill Host Name: localhost
  • fill Port: 2222
  • click Open or press <Enter>

In the black wnidow that appears, type your credentials:


In Mac OS X or Linux, this is done with ssh tool:

ssh -p 2222 user@localhost

Connect to copy files

In Windows, WinSCP is used to copy files to Linux machines. You use the same information as for PuTTY to log in.


In Mac OS X or Linux, the most simple command to copy a file into a home directory of user on a running virtual machine is:

scp -P 2222 myfile user@localhost:~