SMRT Flow Docs

• Introduction
• SMRT Link System High Level Architecture
  • ServiceJob
    • Import DataSet
    • Fasta Reference Convert and Import
    • “Analysis” or “pbsmrtpipe” Job
    • Other Job Types Examples
    • ServiceJob Data Model and Polymorphism
  • DataStore
  • SMRT Link Importing of DataStoreFile(s) from a DataStore
    • PacBio DataSet Overview
    • PacBio Report Overview
    • Accessing Report(s) from SMRT Link Analysis
  • SMRT Link Testing
• smrtflow Tools
  • Commandline Interaction with SMRT Link Services
    • Checking the Status
    • Importing a DataSet into SMRT Link Server
    • Submit an Resequencing Analysis Job
    • Resubmitting an Analysis Job
    • Importing/Converting a RSII movie into SMRT Link
    • Querying Job History
    • Authentication
  • Conversion and Other Tools
    • Fasta to ReferenceSet
    • Convert RSII movie metadata XML to HdfSubreadSet XML
• SMRT Link System Config
  • Common Analysis Configuration
  • SMRT Link Bundle External Resources
  • Testing
• PacBio Parameter “Chemistry” Upgrade Bundle and Services
  • Requirements
  • Example PacBio Data Bundle
  • PacBio Data Bundle Model
  • SMRT Bundle Server
  • Servers
  • Legacy API
  • Building a Stand Alone Chemistry Update Bundle Server
  • Configuration
  • Details of the Root Bundle Dir
  • Building and Starting up the Chemistry Bundle Upgrade Server
  • Getting a List of PacBio Data Bundles from SMRT Link Server
  • Bundles Stored within the SL System install
    • Chemistry Data Bundle Details
  • SMRT Link PartNumbers and Automation Constraints WebService
  • SMRT Link Periodic Checking for Chemistry Data Bundle Upgrades
• SMRT Link Analysis Server APIs
• SMRT Eve Server
  • General Overview
  • System Overview
  • Building, Configuring and Starting up Eve
  • Build
  • Start the Server
  • Eve and SMRT Link Server Tools
  • Tech Support TGZ Bundle
  • Eve WebServices
  • Events/Messages Generated Within SMRT Link Analysis Service
    • How Messages are sent out of SMRT Link to External Server
• Logging in smrtflow
  • Usage
  • Command-Line Example
• PacBio Update Server
  • Requirements
  • Packaging Chemistry Update Bundle Server Build
  • Install
  • Configuration
  • Systemd service definition
  • Upgrade
  • Automated build and deploy
• Web Services CookBook
  • How to get the reports for SMRT Link Job By Id
    • How to get the SMRT Link reports for dataset by UUID
    • How to get QC reports for a particular SMRT Link Run
    • How to get QC reports for a particular Collection
    • How to get recent Runs
    • How to setup a Run in Run Design
    • How to monitor progress of a SMRT Link Run
    • How to capture Run level summary metrics
    • How to setup a job on a particular Collection
    • How to delete a SMRT Link Job
    • How to setup a SMRT Link Analysis Job for a specific Pipeline
    • Querying Job History
• Disclaimer