The Tutorial Data Set

The first thing you need to do is to connect to your virtual machine with the X2Go Client. If you are working with your laptop and haven’t installed it yet - you can get it here: https://wiki.x2go.org/doku.php/download:start

Enter the IP of your virtual machine, the port, the username “ubuntu” and select your ssh key. When you have successfully connected to your machine, open a terminal.

As you have started the VM with a volume attached, this volume needs to be given to the ubuntu user for easy access:

sudo chown ubuntu:ubuntu /mnt/volume/

Create a link in your home directory to the mounted volume:

ln -s /mnt/volume/ workdir

The tutorial dataset is located in our object store. We have also prepared some precomputed results.You can get both here (Group 1):

cd ~/workdir
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group1.tar.gz
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Results_Group1.tar.gz

… and for Group 2:

cd ~/workdir
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Data_Group2.tar.gz
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/nanopore_course_data/Results_Group2.tar.gz

Then, unpack the tar archive:

tar -xzvf Data_Group1.tar.gz
tar -xzvf Results_Group1.tar.gz

or

tar -xzvf Data_Group2.tar.gz
tar -xzvf Results_Group2.tar.gz

and remove the tar archives:

rm Data_Group1.tar.gz
rm Results_Group1.tar.gz
or
rm Data_Group2.tar.gz
rm Results_Group2.tar.gz

Have a short look, on what is contained within the data directory:

ls -l ~/workdir/data/
-rw-r--r-- 1 ubuntu ubuntu 4372654 Aug 30 08:24 Reference.fna
drwxr-xr-x 2 ubuntu ubuntu   24576 Aug 30 08:24 fast5
drwxrwxr-x 2 ubuntu ubuntu    4096 Sep  5 07:23 fast5_small
drwxrwxr-x 2 ubuntu ubuntu    4096 Sep 12 08:01 fast5_tiny
drwxr-xr-x 2 ubuntu ubuntu    4096 Aug 30 08:36 illumina

There are three folders with Nanopore fast5 data, a Reference genome for later comparisons and some illumina data.

If you want to disable system beep sounds:

xset -b