Setup
If you are attending one of our workshops, we will provide a training environment with all of the required software and data.
If you want to setup your own computer to run the analysis demonstrated on this course, you can follow the instructions below.
Note that we use tabsets to provide instructions for all three major operating systems. However, as much as possible we advice you use a Linux system, as our training environment is built on that.
Installing conda
We will perform a fresh installation of the conda package using the miniconda
installation option.
If you already have Miniconda or Anaconda installed, and you just want to upgrade, you should not proceed to making a fresh installation. Just use conda update
to update your existing version of conda.
conda update conda
After updatiing conda, you can proceed to the instructions from number 8 to install mamba into the base environment from the conda-forge channel.
Open a terminal and follow the following instructions:
- Navigate to your home directory:
cd ~
- Download the Miniconda3 installer for mac by running:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
For M1 processor users, you will need to run the below command:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh
- Run the installation script just downloaded:
bash Miniconda3-latest-MacOSX-x86_64.sh
- Follow the installation instructions accepting default options (answering ‘yes’ to any questions)
- If you are unsure about any setting, accept the defaults. You can change them later.
To make the changes take effect, close and then re-open your terminal window.
Test your installation.
- In your terminal window, run the command
conda list
:
conda list
- A list of installed packages appears if it has been installed correctly.
- Remove the installation script as it is no longer needed if successfully installed:
rm Miniconda3-latest-MacOSX-x86_64.sh
- Run the following command to add channels:
conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge; conda config --set channel_priority strict
This adds two channels (sources of software) useful for bioinformatics and data science applications.
- Install Mamba into the base environment from the conda-forge channel with the below command:
conda install mamba -n base -c conda-forge
- Run this to initiate mamba:
mamba init
Open a terminal and follow the following instructions:
- Navigate to your home directory:
cd ~
- Download the Miniconda3 installer for Linux by running:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
- Run the installation script just downloaded:
bash Miniconda3-latest-Linux-x86_64.sh
- Follow the installation instructions accepting default options (answering ‘yes’ to any questions)
- If you are unsure about any setting, accept the defaults. You can change them later.
To make the changes take effect, close and then re-open your terminal window.
Test your installation.
- In your terminal window, run the command
conda list
:
conda list
- A list of installed packages appears if it has been installed correctly.
- Remove the installation script as it is no longer needed if successfully installed:
rm Miniconda3-latest-Linux-x86_64.sh
- Run the following command to add channels:
conda config --add channels defaults; conda config --add channels bioconda; conda config --add channels conda-forge; conda config --set channel_priority strict
This adds two channels (sources of software) useful for bioinformatics and data science applications.
- Install Mamba into the base environment from the conda-forge channel with the below command:
conda install mamba -n base -c conda-forge
- Run this to initiate mamba:
mamba init
Creating conda environments for the workshop
Content will soon be uploaded.
As you may see, all the tools installed have specified version numbers added to the tool names in the format tool=version_numer
. This allows us to install the exact version of tools used for the training.
For your personal use, if you wish to use the latest version of these tools, just omit specifying the version z-version_number` and the latest version of the tool will hopefully be installed.
As you may see, all the tools installed have specified version numbers added to the tool names in the format tool=version_numer
. This allows us to install the exact version of tools used for the training.
For your personal use, if you wish to use the latest version of these tools, just omit specifying the version z-version_number` and the latest version of the tool will hopefully be installed.
Downloading databases
Nextflow
Singularity
You can use Singularity from the Windows Subsystem for Linux (see @wsl).
Once you setup WSL, you can follow the instructions for Linux.
Singularity is not available for Mac OS.
These instructions are for Ubuntu or Debian-based distributions1.
sudo apt update && sudo apt upgrade && sudo apt install runc
CODENAME=$(lsb_release -c | sed 's/Codename:\t//')
wget -O singularity.deb https://github.com/sylabs/singularity/releases/download/v3.10.2/singularity-ce_3.10.2-${CODENAME}_amd64.deb
sudo dpkg -i singularity.deb
rm singularity.deb
Visual Studio Code
- Go to the Visual Studio Code download page and download the installer for your operating system. Double-click the downloaded file to install the software, accepting all the default options.
- After completing the installation, go to your Windows Menu, search for “Visual Studio Code” and launch the application.
- Go to “File > Preferences > Settings”, then select “Text Editor > Files” on the drop-down menu on the left. Scroll down to the section named “EOL” and choose “\n” (this will ensure that the files you edit on Windows are compatible with the Linux operating system).
- Go to the Visual Studio Code download page and download the installer for Mac.
- Go to the Downloads folder and double-click the file you just downloaded to extract the application. Drag-and-drop the “Visual Studio Code” file to your “Applications” folder.
- You can now open the installed application to check that it was installed successfully (the first time you launch the application you will get a warning that this is an application downloaded from the internet - you can go ahead and click “Open”).
- Go to the Visual Studio Code download page and download the installer for your Linux distribution. Install the package using your system’s installer.
R and RStudio
- Go to the R installation folder and look at the instructions for your distribution.
- Download the RStudio installer for your distribution and install it using your package manager.
Workshop Data
Footnotes
See the Singularity documentation page for other distributions.↩︎