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CCMS Deployments

These are the utility scripts/make files to get a deployment working for CCMS workflows in ProteoSAFe

Necessary Steps To Get Working

  1. Create a new repository to hold your workflows (e.g. GNPS_Workflows or Proteomics_Workflows).
  2. Import CCMSDeployments as a submodule (git submodule add https://github.com/CCMS-UCSD/CCMSDeployments.git)
  3. Link the following files into the root folder: fabfile.py, Makefile.deploytemplate, workflow_validator.py and create yml files similar to the following for each server (or just copy from fabric-production-gnps.yml, fabric-production-proteomics.yml, fabric.yml as examples)
debug: true    # leave this alone

run:           # leave this alone
 warn: true 
 echo: true 
 
production:    # only add this section if you intend to deploy with sudo
 tool_user: gamma 
 workflow_user: ccms
 user: ccms
 
workflows:     # workflows to be deployed
 - fast_test_workflow
 
paths:         # paths for tools and workflows on the server to be deployed to
 tools: /data/cluster/tools
 workflows: /ccms/workflows
  1. Create a Makefile.credentials with the USERNAME key for your username credentials on the particular server in the root folder (do not check this in)

To Deploy a Single Test Workflow

Navigate to the fast_test_workflow directory and execute one of the following:

  1. make deploy-debug to deploy to proteomics2
  2. make deploy-debug-update to deploy to proteomics2 and update the default
  3. make deploy-production-gnps to deploy to gnps and update the default
  4. make deploy-production-gnps-pre to deploy to gnps
  5. make deploy-production-proteomics to deploy to proteomics and update the default
  6. make deploy-production-proteomics-pre to deploy to proteomics

To Deploy All Test Workflows

For proteomics2 (using the default configuration), execute:

fab2 -H <username>@proteomics2.ucsd.edu --prompt-for-login-password deploy-all.

For production servers {proteomics,gnps}, execute:

fab2 -H <username>@<server>.ucsd.edu --prompt-for-login-password --prompt-for-sudo-password deploy-all --config fabric-production-<server>.yml