All of the software needed to complete assignments and tutorials is available through servers running on the nectar cloud1.
Students enrolled in the subject can access these cloud servers using any computer with a web browser (tested on Chrome and Safari).
https://rstudio.bioinformatics.guide
Use the username and password provided to you by the subject coordinator.
This is the default option for all students as it will work on any modern computer and doesn’t require you to install any software.
If you prefer to use your own computer for the subject you are welcome to do so. This should be possible regardless of what type of computer you have, but it will be slightlier easier on a mac or linux machine. See below for extra steps on windows.
All of the software used in this subject is freely available and most can be installed relatively easily using the conda package manager.
Follow the installation instructions to install miniconda for your operating system. Choose the version for python 3
On my mac this was accomplished as follows;
wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh
After doing this you should setup channels as follows
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
You should now be able to install software required for all the tutorials and assignments. For example
conda install mafft
echo "PATH=\"$HOME/miniconda3/bin:$PATH\"" > ~/.Renviron
In order to run the automated tests for unix commands you will need to install the appropriate testing framework.
MacOS
Installation can be using the homebrew package manager. First follow instructions at https://brew.sh/ to install homebrew. Then install bats using
brew install bats-core
Install additional bats libraries like this
cd
mkdir -p ~/.local/bin
mkdir -p ~/.local/lib
cd ~/.local/lib
git clone https://github.com/ztombol/bats-support bats-support
git clone https://github.com/ztombol/bats-assert bats-assert
Windows or Linux
If using windows first install Windows subsystem for linux and open a new terminal window
Run the following code to install bats in ~/.local
cd
mkdir -p ~/.local/bin
mkdir -p ~/.local/lib
git clone https://github.com/bats-core/bats-core.git
cd bats-core
./install.sh ~/.local/
cd ~/.local/lib
git clone https://github.com/ztombol/bats-support bats-support
git clone https://github.com/ztombol/bats-assert bats-assert
You will now need to make sure that bats is on your PATH.
echo "export PATH=\"\${HOME}/.local/bin:\$PATH\"" >> ~/.bashrc
Check that this worked by looking at the bottom few lines of your .bashrc file.
tail ~/.bashrc
You should see a line that reads
export PATH="${HOME}/.local/bin:$PATH"
For this to take effect you will need to close your current Terminal window and reopen. After opening a new terminal window try running bats like this
bats
It should show some help text if it is installed.
Although RStudio allows you to access the terminal from its interface it doesn’t actually come bundled with the software required to run the terminal itself. On Mac and Linux machines this is built-in to the operating system. On windows you have several options for installing this;
If you have Windows 10 you can use windows subsystem for linux following these instructions (from Ulrik Horn);
If don’t have Windows 10 you may be able to get things working by installing git bash or another unix layer on top of windows. At this stage I am unsure if these will work for all exercises since they may not be complete unix systems.