# wf-metagenomics install guide (Unix) ## 1. Install docker ``` sudo apt install docker.io ``` Give docker the proper permissions: ``` sudo usermod -aG docker $USER ``` Check that docker works: ``` sudo docker run hello-world ``` Check that install works without ```sudo```: ``` docker run hello-world ``` If it's not the case, try: ``` newgrp docker ``` If the install doesn't work, you can try the more convoluted method here: https://docs.docker.com/desktop/install/ubuntu/ ## 2. Install nextflow If ```curl``` is not installed, start with: ``` sudo snap install curl ``` Then run: ``` curl -s https://get.nextflow.io | bash sudo mv nextflow /usr/local/bin ``` ## 3. Install the wf-metagenomics workflow To install the workflow, run: ``` nextflow run epi2me-labs/wf-metagenomics --help ``` You will find the wf-metagenomics folder in ```.nextflow/assets/epi2me-labs/```. You will find some test data inside. Run the workflow on the test data to make sure it works: ``` nextflow run epi2me-labs/wf-metagenomics --fastq test_data --kraken2 ``` If it does not work, you might have to update the workflow with: ``` nextflow drop epi2me-labs/wf-metagenomics ``` You might also need to re-run the docker permissions: ``` sudo usermod -aG docker $USER newgrp docker ```