This document describes the setup for a VirtualBox virtual machine to be used as the base installation for working through the training materials in this course.
We make available a virtual machine image at zenodo (doi:10.5281/zenodo.1184095) which should be sufficient to run the course materials.
- Course VM: download
The username for this VM is ibioic and the password is ibioic-course.
We base our VM on the basic Ubuntu 16.04 LTS installation, obtained from this site. The VM image was built and software/materials installed by the course tutors. The system is set by default to use 4GB of the host system RAM, and 128MB of video memory, but this can be modified in the VirtualBox software.
The VirtualBox software can be downloaded for your operating system from this page.
Once you have downloaded the application, please follow the instructions relevant for your system to install.
For the course VM, you will also need to install the VirtualBox Extension Pack, available here.
Under some circumstances you may find that you need to increase the HDD size, though this should not be necessary to complete the course materials:
- Shut down the VM
- Resize the HDD:
VBoxManage modifyhd <path_to_vdi> --resize <size_in_MB> - Mount a Ubuntu Live CD on the VM and boot into it
- Use
gpartedto resize OS partitions.
You might also wish to reduce the size of the virtual HDD on your system (without resizing), by writing zeros to unused space, and compressing:
- On the VM, issue:
sudo dd if=/dev/zero of=/emptyfile bs=1Mto write zeros in an empty file, then remove the empty filesudo rm /emptyfile - Shut down the VM
- Compact the HDD:
VBoxManage modifyhd <path_to_vdi> --compact
Once the users are logged into their accounts, they need to change directory to the repository root, and activate the conda environment:
$ cd 2018-03-06-ibioic
$ source actvate 2018-03-06-ibioic
This will modify the user prompt to reflect the active virtual machine, and from this point all teaching materials should work.
In addition to the tools that were available with the base VM, we have installed:
apt-get was updated with
sudo apt-get updateand the aptitude interface onto apt-get:
sudo apt install aptitudegit is required to obtain the most up-to-date version of the course materials.
sudo apt install gitopenssh-server enables secure remote logins
sudo apt install openssh-serverpandoc converts markup documents between formats, and is used to produce course output from the markdown source
sudo apt install pandocAs part of the VM setup, we need the ability to create new users and passwords for them. This requires mkpasswd, part of whois.
sudo apt install whoisArtemis and ACT are widely-used genome annotation tools.
BLAST is the ubiquitious tool used to search for similar sequences in a database. We install a local command-line version.
sudo aptinstall ncbi-blast+clustal omega is a widely-used sequence alignment package
sudo apt install clustaloHMMer is a hidden Markov model-based tools for sequence profile generation and searching against databases.
sudo apt install hmmerJalview is a widely-used sequence alignment visualisation tool
sudo apt install jalviewJMol is a widely-used structural biology and protein structure visualisation tool
sudo apt install jmolmuscle is a widely-used sequence alignment package
sudo apt install musclepymol is a widely-used structural biology and protein structure visualisation tool
sudo apt install pymolsamtools is the standard package for converting and manipulating short-read sequencing data
sudo apt install samtoolst-coffee is a widely-used sequence alignment package
sudo apt install t-coffeeVSEARCH is a fast alternative to BLAST+
sudo apt install vsearch