Nextflow Template

To run the workflow to test simply do

make run

To learn NextFlow checkout this documentation:

https://www.nextflow.io/docs/latest/index.html

Installation

You will need to have mamba, and nextflow installed to run things locally.

Broadly recommend installing mamba from mamba installed and then using mamba to install nextflow

Running Local Test

Getting test data

cd data
sh ./get_data.sh

Running the test case

make run_test

or more explicitly so you can see what you can edit

nextflow run nf_workflow.nf -resume \
	-c nextflow_test.config \
	--parallel_files "YES" \
	--extract "NO" \
	--maxfilesize 100 \
	--cache_dir "${PWD}/data/cache" \
	--input_spectra "${PWD}/data/data" \
	--query "QUERY scaninfo(MS2DATA)"

Deployment to GNPS2

In order to deploy, we have a set of deployment tools that will enable deployment to the various gnps2 systems. To run the deployment, you will need the following setup steps completed:

1. Checked out of the deployment submodules
2. Conda environment and dependencies
3. SSH configuration updated

Checking out the deployment submodules

use the following commands from the deploy_gnps2 folder.

You might need to checkout the module, do this by running

git submodule init
git submodule update

You will also need to specify the user on the server that you've been given that your public key has been associated with. If you want to not enter this every time you do a deployment, you can create a Makefile.credentials file in the deploy_gnps2 folder with the following contents

USERNAME=<enter the username>

Deployment Dependencies

You will need to install the dependencies in GNPS2_DeploymentTooling/requirements.txt on your own local machine.

One way to do this is to use conda to create an environment, for example:

conda create -n deploy python=3.8
pip install -r GNPS2_DeploymentTooling/requirements.txt

SSH Configuration

Also update your ssh config file to include the following ssh target:

Host ucr-gnps2-dev
    Hostname ucr-lemon.duckdns.org

Deploying to Dev Server

To deploy to development, use the following command, if you don't have your ssh public key installed onto the server, you will not be able to deploy.

make deploy-dev

Deploying to Production Server

To deploy to production, use the following command, if you don't have your ssh public key installed onto the server, you will not be able to deploy.

make deploy-prod