GNPS ProteoSAFe Workflows

This public repository contains the GNPS Workflows running on GNPS (http://gnps.ucsd.edu).

Contribute to GNPS

The GNPS community is always welcoming suggestions and contributions. Be part of the community and contribute !

GitHub Repositories

Your are kindly invited to open "issues" on our GitHub repositories, and propose changes to our Documentation and Workflows. We are also welcoming direct pull request on the respective repository.

GNPS_Documentation GitHub respository that points to the documentation website (https://ccms-ucsd.github.io/GNPSDocumentation).

• https://github.com/CCMS-UCSD/GNPSDocumentation

GNPS_Workflows Present GitHub repository that contains the workflows available on GNPS (http://gnps.ucsd.edu):

• http://github.com/CCMS-UCSD/GNPS_Workflows

GNPS Forum

Discussions and suggestions can also take place on the GNPS forum at https://groups.google.com/forum/#!forum/molecular_networking_bug_reports.

GNPS Core Webserver Status

GNPS Integration Web and Workflow jobs are handled in the CCMS-Integration-Tests Repository.

Feature	Server Status
GNPS/Beta/MassIVE API Tests
GNPS External API Tests
GNPS/Beta/MassIVE Selenium Tests
GNPS Workflows Fast Test
Beta Workflows Fast Test
GNPS Full Workflows Test
Beta Full Workflows Test

Uptime Robot Monitor - https://stats.uptimerobot.com/Am4PLUWn3

Specific Workflow Tests

Workflow	GNPS Link	Beta Link	Unit Test
Molecular Networking	Workflow	Workflow
Large Scale Library Search	Workflow	Workflow	---
MASST	Workflow	Workflow	---
Feature-Based Molecular Networking	Workflow	Workflow
MS2LDA Motif DB	Workflow	Workflow
MolNetEnhancer/MetaboDistTree	Workflow	Workflow
MSMS-Chooser	Workflow	Workflow	---
OpenMS Feature Detector for FBMN - Future Feature	[Workflow]()	[Workflow]()	---
MSHub-GC Deconvolution	Workflow	Workflow
Library Search/Molecular Networking GC	Workflow	Workflow
Merge Polarity Networks	Workflow	Workflow
Microbiome-Metabolomics Association - mmvec	Workflow - Inactive	Workflow	---
Sirius - Bocker Lab	Workflow	Workflow	---
Qemistree	Workflow	Workflow	---
LC - MZMine2	Beta Workflow	Workflow	---
Legacy Networking	Workflow	---	---
Legacy Library Search	Workflow	---	---

GNPS Documentation

Build:

GNPS Microservices Links/Status

Link	Description	Status
gnps-external.ucsd.edu	Linking out structures to external services (e.g. NPAtlas)
gnps-classyfire.ucsd.edu	Classyfire caching proxy for GNPS
gnps-structure.ucsd.edu	Structure processing worker
redu.ucsd.edu	Reuse of Public Data/Sample Information
gnps-quickstart.ucsd.edu	GNPS Quickstart Server
gnps-cytoscape.ucsd.edu	GNPS Cytoscape Export/Styling Server
masst.ucsd.edu	GNPS MASST Query Server
metabolomics-usi.ucsd.edu	Metabolomics USI Server

Testing

Unit Testing

We have a limited number of unit tests for GNPS workflows. A test folder can be found in each workflow folder.

To run all unit tests on a consistent platform as github actions, we use act.

make test-push-full

We also have targets for individual tests, e.g.:

make test-fbmn

Inside the test folder, we recommend use the testing tool nose2. Execute the following code to run the workflow specific tests

nose2 -v

Integration Testing

In order to add specific examples of workflow on GNPS to make sure they are tested periodically, you can add to our test files. Specifically for each workflow we have a list of test tasks that we clone and run every 12 hours. These can be found in the test-integration-workflow folder for each workflow.

Workflow Deployments

In order to deploy workflows, we have included the workflow deployment packages from CCMS. Specifically, we will want to follow the guide here.

Once you have checked out this repository, make sure to have all the submodules checked out as well. Then you will need to follow these steps.

Then we can get a workflow onto proteomics2. To test it without over-writing the default version, you can use this command for any workflow you would like to deploy:

cd <workflow folder>
make deploy-debug

as outlined here.