Developer’s Reference

• 1. Setup
  • 1.1. Prerequisites and general notes
  • 1.2. Setup procedure
  • 1.3. Configuration of CCP4 Cloud Clients
  • 1.4. Maintenance and Updates
  • 1.5. Contact
  • 1.6. Appendix A. Installation of CCP4
  • 1.7. Appendix B. Adjusting configuration file for Number Cruncher Servers
  • 1.8. Appendix C. Adjusting configuration file for the Front-End Server
  • 1.9. Appendix D. Adjusting start script for Number Cruncher Servers
  • 1.10. Appendix E. Adjusting start script for the Front-End Server
  • 1.11. Appendix F. Adjusting Apache configuration on host machines
  • 1.12. Appendix G. Tests and checks
  • 1.13. Appendix H. Creating 1st user with administrative privileges
• 2. CCP4 Cloud Launch Scripts
  • 2.1. Launch script for Front-End Server
  • 2.2. Launch script for Number Cruncher
  • 2.3. Update script
• 3. CCP4 Cloud Configuration
  • 3.1. Configuration file structure
  • 3.2. Configuration of the Front End Server
    • 3.2.1. FE Server Configuration Items
  • 3.3. Configuration of the Client Proxy Server
    • 3.3.1. Client Proxy Server Configuration Items
• 4. Managing CCP4 Cloud with PM2
  • 4.1. What is PM2?
  • 4.2. Setup/Launcher script
  • 4.3. Installing/Setup
    • 4.3.1. The start.d folder
    • 4.3.2. The ecosystem.config.js configuration
    • 4.3.3. The Front End or Number Cruncher config.json
  • 4.4. Launching a Front End or Number Cruncher
    • 4.4.1. Installing PM2
    • 4.4.2. Managing CCP4 Cloud with PM2
    • 4.4.3. Starting CCP4 Cloud on system boot
  • 4.5. Useful PM2 commands
• 5. Configuration of CCP4 Cloud with Nginx
• 6. Linking AlphaFold setup with CCP4 Cloud
  • 6.1. Structure prediction in CCP4 Cloud
  • 6.2. Linking AlphaFold setup in outline
  • 6.3. Appendix A. AlphaFold setup
  • 6.4. Appendix B. ColabFold setup
  • 6.5. Appendix C. OpenFold setup
  • 6.6. Appendix D. JSON-formatted configuration file
• 7. Linking MrParse to local databases
  • 7.1. MrParse search in CCP4 Cloud
  • 7.2. Configuring MrParse to use local resources
• 8. Task Interface Description
  • 8.1. Parameter Description
    • 8.1.1. Common description items
    • 8.1.2. Combobox
    • 8.1.3. Integer Input
    • 8.1.4. Text Area
• 9. CCP4 Cloud Task Development: Hello World!
  • 9.1. CCP4 Cloud source code structure
  • 9.2. “Hello, World!” task in stages
    • 9.2.1. Create Task Class
    • 9.2.2. Create Task Documentation
    • 9.2.3. Insert New Task in the Task List
    • 9.2.4. Making the Task Driver
• 10. Software testing in CCP4
  • 10.1. Unix scripts
  • 10.2. Pytest
    • 10.2.1. Test new build manually
• 11. CCP4 Cloud tests
  • 11.1. Data for Cloud tests
  • 11.2. Inventory
• 12. CCP4 Cloud Client Setup
  • 12.1. MS Windows
  • 12.2. Linux
  • 12.3. Mac OSX
• 13. What is CCP4 Cloud Client Software
  • 13.1. Do I have to have CCP4 Cloud Client installed?
  • 13.2. How do I use CCP4 Cloud Client once it is installed?
• 14. How to add a new Sphinx theme

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