Installation¶
MIAAIM is implemented in nextflow, which requires Java 8 or later. To install MIAAIM on your machine, follow the steps below for your operating system:
Linux / OS X¶
1. Install Docker
and ensure that it is available to your system using the command docker images
2. Install Nextflow
using curl -s https://get.nextflow.io | bash
3. You can check that Nextflow is installed by calling it in the context of the
directory that you installed it in with ./nextflow run.
4. (Recommended) If you want to be able to call Nextflow directly from the command line without entering the path to it, enter the follwing command:
chmod +x nextflow # be able to call nextflow
Windows¶
To run Nextflow in Windows, you will need to install WSL prior to installing Nextflow. To do this, follow these steps:
Open Windows Powershell as administrator
2. Download WSL by typing
dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
3. Enable virtual machine by typing
dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
4. Download the latest Linux kernel update package
Set WSL2 as your default kernel by typing
wsl --set-default-version 2
6. Install linux distribution – we have tested MIAAIM successfully using Ubuntu 20.04 LTS
7. Open your Ubuntu installation (you will be asked to set up your installation by providing a user name and password)
8. Within the Ubuntu shell enter the following commands to install necessary components for Nextflow and pulling the MIAAIM repository from GitHub:
sudo apt update # upgrade packages
sudo apt install openjdk-14-jre-headless # install latest version of Java
curl -s https://get.nextflow.io | bash # install latest version of Nextflow
chmod +x nextflow # be able to call nextflow
sudo apt-get -y install git # install git so you can clone MIAAIM from GitHub
sudo apt-get install -y libarchive-tools # install bsdtar command for unzipping prototype image
9. Now install Docker for windows and allow it to connect with your WSL2 (see here for details)
You should now be able to run nextflow and MIAAIM within your installed WSL as you would with a Linux system (above) starting at step 3!
Tip
You can transfer data to and from your WSL by using the /mnt folder.
For example, once inside your WSL, the following command will transfer the
data-example folder from the D drive on your windows machine to your home folder
within the WSL:
cp -r /mnt/d/data-example ~/ # copy data to WSL from D drive