Using the VirtualBox image

You can download a VirtualBox image from EI’s opendata site. This is a complete virtual computer system that includes an Ubuntu operating system, NanoOK, all the dependencies and an example data set.

NOTE: Currently, this image only includes the LAST aligner. If you wish to use an alternative aligner, you will need to download that to the VM. In future releases, we hope to include other alignment tools.

  • To run it, you will need to have installed the free VirtualBox software - it’s available from virtualbox.org.
  • When you start the image, it will boot into an Ubuntu desktop. You can click on the Terminal icon on the left hand side and start typing commands.
  • The screen display is quite small - this is because Oracle (owners of VirtualBox) do not license users to distribute additional components known as the “Guest Additions”. However, you can download this for free and install it yourself - see the VirtualBox manual for details.
  • You also need to install the Guest Additions before you can share folders with the host operating system.
  • There is one user setup called ‘nanook’ and the password is also ‘nanook’.

To run the example dataset (consisting of only 500 reads) with NanoOK, do the following:

  1. Start the VirtualBox image.

  2. Open a terminal and type:

    cd ~/Documents/NanoOK\_Example

  3. To index the reference, type:

    cd references
lastdb -Q 0 ecoli\_dh10b\_cs ecoli\_dh10b\_cs.fasta
cd ..

  4. To extract, type:

    nanook extract -s N79596\_dh10b\_8kb\_11022015 -t 2

  5. To align, type:

    nanook align -s N79596\_dh10b\_8kb\_11022015 -r references/ecoli\_dh10b\_cs.fasta -t 2

  6. To analyse, type:

    nanook analyse -s N79596\_dh10b\_8kb\_11022015 -r references/ecoli\_dh10b\_cs.fasta -passonly -t 2

  7. To view the PDF, use the “Files” icon in the left-hand toolbar of the Ubuntu desktop and browse to Documents->NanoOK_Example->N79596_dh10b_8kb_11022015->latex_last_passonly and double-click on the PDF file. Note, that as this example consists of such a small number of reads, the graphs will not be quite as informative as for a full dataset.

When new versions of NanoOK are released, you don’t need to download another VM image. Instead type the following inside a Terminal window to install the latest version:

cd ~/Documents/NanoOK
git pull