OLD_METHOD.md

Installation and tutorial

This pipeline supports many cloud platforms and cluster engines. It also supports docker, singularity and Conda to resolve complicated software dependencies for the pipeline. A tutorial-based instruction for each platform will be helpful to understand how to run pipelines. There are special instructions for two major Stanford HPC servers (SCG4 and Sherlock).

• Cloud platforms
  • Web interface
    • DNAnexus Platform
  • CLI (command line interface)
    • Google Cloud Platform
    • DNAnexus Platform
• Stanford HPC servers (CLI)
  • Stanford SCG4
  • Stanford Sherlock 2.0
• Cluster engines (CLI)
  • SLURM
  • Sun GridEngine (SGE/PBS)
• Local Linux computers (CLI)
  • Local system with singularity
  • Local system with docker
  • Local system with Conda
• Local Windows computers (CLI)
  • Windows 10 Pro with docker
  • Windows 10 Pro/Home with Conda

Output directories

Output directory specification