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Installation

Install Nextflow

If not already installed, install Java: https://adoptopenjdk.net/

Expand to see troubleshooting tips related to Java
  • If nextflow has trouble interacting with your java, we recommend checking the version number with java --version
  • Some errors have been occurring with version numbers with four components (i.e. 11.0.14.1). If your version has four components, consider downloading an archived version, such as “11.0.14+9”, from https://adoptium.net/archive.html?variant=openjdk11 as a temporary solution until this issue is resolved.

Install Nextflow: curl -s https://get.nextflow.io | bash

This command will create a nextflow executable in the current directory. To simplify usage, consider moving this executable to a directory that is available on $PATH. One common place for this is a bin/ directory in your home folder:

mkdir -p ~/bin                                      # Creates a bin directory in the home folder
mv nextflow ~/bin                                   # Moves nextflow to that directory
echo $SHELL                                   	    # Determine what shell is used by your terminal 

If your terminal uses bash, the following commands should work as is.
Replace .bashrc with .zshrc in these commands, if your terminal uses zsh instead (often the case on Mac OS X).

echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc   # Make the directory accessible on $PATH
source ~/.bashrc                                    # Reload the shell configuration

Verify that Nextflow is accessible by going to your home directory (cd ~) and typing nextflow on the command line. This should automatically print the help menu.

Install Docker*

Install Docker. Ensure that the Docker engine is running by typing docker run hello-world. If the engine is running, you should see “This message shows that your installation appears to be working correctly.” in the output.

* Harvard Medical School users using the O2 Compute Cluster should not install Docker - learn more here.


Ready to run??

Beginners, start with the tutorial

Experienced users can go to the MCMICRO Reference Sheet