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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).

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

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 web-ccms-api
GNPS External API Tests web-external-api
GNPS/Beta/MassIVE Selenium Tests web-ccms-selenium
GNPS Workflows Fast Test workflow-proteomics3-fast
Beta Workflows Fast Test workflow-proteomics3-fast
GNPS Full Workflows Test workflow-gnps
Beta Full Workflows Test workflow-beta

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 workflow-unit-ms2lda
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.