To run the workflow to test simply do
make run
To learn NextFlow checkout this documentation:
https://www.nextflow.io/docs/latest/index.html
Make sure the mgf file you want to work with is under data and has the extensions .mgf
Then, just run the script run.sh if you have everything installed properly
The script gets all the library files and stores them under data/libraries/
The script will also run the pipeline twice to finish the library search workflow (some issues with this hence it has to run twice)
The final result tree (in json format) is in nf_output/final_tree.json
You will need to have conda, mamba, and nextflow installed to run things locally.
Check the definition for the workflow input and display parameters: https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/workflowdev/
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:
- Checked out of the deployment submodules
- Conda environment and dependencies
- SSH configuration updated
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>
You will need to install the dependencies in GNPS2_DeploymentTooling/requirements.txt on your own local machine.
You can find this here.
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
Also update your ssh config file to include the following ssh target:
Host ucr-gnps2-dev
Hostname ucr-lemon.duckdns.org
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
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