Installation for Course Attendees

This document will describe the process for setting up and testing course materials, in preparation for attendance at the workshop.

Two different setups are described:

1. Installation of all components on your own local machine
2. Download and use of a Linux virtual machine

Either one of these will prepare your machine for the workshop.

We prefer that attendees install materials on their own laptops for the course, as the software and learning materials will then persist and be usable/re-usable on your own machine after the course itself is complete. The virtual machine is a “Plan B” that should be usable on any machine, and is intended as the fallback in case of installation problems on your own laptop.

Important

You should install all the software and/or the virtual machine before you attend the course. This will save you, and everyone else at the course, time at the beginning of the first day, and give more time to explore advanced topics in the workshop.

We will offer an online hangout to help with installation problems, just before the course. Your course organiser will provide information about this.

The process of installing the required software on your machine is as follows:

1. Install Anaconda on your computer (if it is not already present).
2. Install git on your computer (if it is not already present).
3. Obtain the course materials.
4. Install Python requirements.
5. Install third-party software tools.
6. Test the installation.

The process of installing the virtual machine is as follows:

1. Install VirtualBox on your computer.
2. Download the course virtual machine and open it in VirtualBox.

1. Install all components on your local machine

1. Install Anaconda on your computer

For ease of installation and consistency, we install as much as is practical using the Anaconda environment. This is cross-platform software that works on Windows, macOS and Linux, and provides several essential components for the course, such as Python and the common Jupyter notebook interface that will be used.

If you do not already have Anaconda installed on your system, please follow the instructions at the page below:

• Anaconda installation

2. Install git on your computer

If you do not have a working copy of git installed on your machine, install one now by following instructions at the page below.

• git installation

Note

If you are using Windows, you will be installing git bash which, as well as git, provides the Bash terminal environment that you will be using during the course. This provides an experience very similar to working at the terminal in Linux/macOS.

3. Install the course materials

You will need to clone the course material repository to your own machine.

Using the terminal [1], navigate to a convenient location (e.g. your Desktop). Then clone the course repository with the command:

git clone https://github.com/widdowquinn/2018-03-06-ibioic.git

Note

This will create a new directory called 2018-03-06-ibioic, containing the course materials.

Change to the course material directory in your terminal with the command:

cd 2018-03-06-ibioic

4. Install Python requirements

To install the Python module requirements for the course, issue the command below in the terminal [1]:

pip install -r requirements_students.txt

5. Install third-party software

BLAST and MUSCLE do not require JAVA, and can be set up independently:

1. Install BLAST

BLAST is a tool for searching with a protein or nucleotide sequence against a database of other biological sequences.

• BLAST installation instructions

2. Install MUSCLE

MUSCLE is a program for multiple sequence alignment.

• MUSCLE installation instructions

ARTEMIS, JALVIEW and JMOL require the JAVA VM, so JAVA must be installed first:

3. Install JAVA

JAVA is a programming language that runs on a virtual machine (the JVM). Several bioinformatics tools are written in JAVA, and require the JVM to be installed in order to run.

• JAVA installation instructions

4. Install ARTEMIS

ARTEMIS is a genome sequence browser and editor.

• ARTEMIS installation instructions

5. Install JALVIEW

JALVIEW is a sequence alignment viewer and editor.

• JALVIEW installation instructions

6. Install JMOL

JMOL is a program for visualising biological molecules (e.g. proteins).

• JMOL installation instructions

7. Test the tools/materials

To make sure that the downloaded tools are installed and working on your machine, please follow the instructions on the testing your installation page.

• Testing your installation

2. Download and use a Linux virtual machine

1. Install VirtualBox on your computer

VirtualBox is a program that allows you to run virtual machines on your own computer. Virtual machines are software implementations of operating systems that run as if they are a separate computer.

We have provided a virtual machine pre-loaded with software and course materials, as a fallback in case of installation difficulties on your own machine. To install the VirtualBox program, please follow the instructions on the linked page.

• Install VirtualBox

2. Download and import the course virtual machine

We provide a Linux virtual machine pre-loaded with course materials and the required software, which can be used to participate in the workshop.

Attention

The virtual machine file is very large (11GB) and should be downloaded well in advance of the workshop, if you think you may need to use it!

Click on the badge below to go to the virtual machine download page:

Click on the link for 2018-03-06-ibioic.vdi to download the virtual machine in a suitable location.

Warning

This may take some time to download!

Click on the link for 2018-03-06-ibioic.vbox to download the VirtualBox file in the same location as the .vdi file.

Add the virtual machine.

• Click on Machine in the VirtualBox menu bar
• Click on Add
• Navigate to the .vbox file you just downloaded, and select it
• Click on Open

You should see the 2018-03-06-ibioic machine in the list at the left hand side of the application.

Start the virtual machine.

• Select the new IBioIC virtual machine (2018-03-06-ibioic)
• Click on the Start button in VirtualBox

The virtual machine will start as a new window, and appear to be booting up. When this process is complete, it will present you with a login screen. Use the following credentials to log in:

• Username: ibioic
• Password: ibioic-course

On successful login, you will see a standard Ubuntu desktop, and will be ready to begin the course.

[1]	(1, 2) The terminal means git bash on Windows, and Bash on Linux/macOS.