2. Local installation¶

If you can not access Gitpod you can also install everything locally.

Some requirements may be different depending on your local machine.

2.1 Requirements¶

Nextflow can be used on any POSIX-compatible system (Linux, macOS, Windows Subsystem for Linux, etc.).

Requirements

Optional requirements

Singularity 2.5.x (or later)
Conda 4.5 (or later)
Graphviz
AWS CLI
A configured AWS Batch computing environment

2.2 Download Nextflow¶

Execute this command in your terminal:

wget -qO- https://get.nextflow.io | bash

Alternatively, you could use the curl command:

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

Next, ensure that the downloaded binary is executable:

chmod +x nextflow

Finally, ensure the nextflow executable is in your $PATH. The executable could be in /usr/local/bin, /bin/, etc.

2.3 Docker¶

Ensure you have Docker Desktop running on your machine. You can download Docker here.

2.4 Training material¶

You can view the training material here.

To download the material, execute this command:

git clone https://github.com/nextflow-io/training.git

Then cd into the nf-training directory.

2.5 Checking your installation¶

Check that you have correctly installed nextflow by running the following command:

nextflow info

This should print the current version, system, and runtime.

Exercise

To test that the environment is working correctly, execute the following command:

nextflow info

This should come up with the Nextflow version and runtime information:

Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC
System: Linux 6.1.75-060175-generic
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src
Encoding: UTF-8 (UTF-8)