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Nanopore Dunedin

Genomics Aotearoa ONT MinION workshop

This markdown file will be turned into a proper html at some point, but for now…

Virtual boxes for nanopore sequencing analysis

For the data analysis component of the workshop we will be running the analysis through a virtual box.
This allows you to familiarise yourself with the server-like interface on your own Desktop, with all the tools installed.

Installation of Vagrant

Head to Vagrant and follow the instructions.

Option 1 - preferred: Downloading the VM.

The VM has been uploaded to the Vagrant cloud, we can download it using the following commands.

  1. Create the VM directory
    • mkdir -p ~/Vagrant/nanopore_dunedin/
  2. Change into the VM directory
    • cd ~/Vagrant/nanopore_dunedin/
  3. Generate the relevant Vagrant file
    • vagrant init alexiswl/nanoporeVM
    • If you cannot find the vagrant command, try logging out and back in again
  4. Download the vagrant box.
    • vagrant up
    • This will redirect you to cloudstor. The file is a few Gbs, please be patient.
  5. SSH into the vagrant box.
    • vagrant ssh
    • You should now be user vagrant@xenial_ont
    • xenial is the ‘codename’ for Ubuntu 16.

Option 2 - alternative: Using the provided USB stick.

Windows users should open up Git Bash, MacOSX and Ubuntu users can use terminal

  1. Create the VM directory
    • mkdir -p ~/Vagrant/nanopore_dunedin/
  2. Change into the VM directory
    • cd ~/Vagrant/nanopore_dunedin/
  3. Move across the Vagrant box from the USB onto your computer.
    • `vagrant box add alexiswl/nanoporeVM /localpath/to/vagrant-box.box
  4. Generate the relevant Vagrant file
    • vagrant init alexiswl/nanoporeVM
    • *If you cannot find the vagrant command, try logging out and back in again.
  5. SSH into the vagrant box.
    • vagrant up
    • vagrant ssh
    • You should now be user vagrant@xenial_ont
    • xenial is the ‘codename’ for Ubuntu 16.

Shared folders

By default, /vagrant on the VM is the mounted onto ~/Vagrant/nanopore_dunedin.
We can use this to visualise and input our data.

Running through Jupyter (advanced users)

For those that are fans of having a documented version of their analysis, Jupyter is installed on the VM, however you will need to configure the vagrant file accordingly.
See this link for more details.