Prenacs

• Prenacs
  • Key concepts
  • Related libraries
  • Usage
  • Acknowledgements
• Prenacs User manual
  • Implementing a plugin
    • Checking the plugin implementation
  • Database setup
  • Managing the attributes
    • Attribute metadata
    • Example
    • Changing attribute metadata by constant datatype and computation group
    • Changing attribute metadata with different datatype and computation group
  • Batch computing
  • Running on a Slurm cluster
    • Input entities provided as a set of identifiers
      • Computed entity IDs
    • Input entities provided as a set of input files
    • Incremental computations
    • Computation parameters
    • Computation state
      • State initialization parameters
    • Report file metadata
  • Loading the computation results
• ProvBatch: Plugin implementation guide
  • Public Interface of ProvBatch plugins
    • Compute function
    • Metadata constants
    • Common resources for batch computations
      • Creating common resources
      • Accessing common resources
      • Finalizing common resources
  • Non-Python plugins
    • Nim plugins
    • Rust plugins
• MultiPlug
  • Features
  • Installation
  • Usage
• MultiPlug: Usage manual
  • Importing a plugin module
  • Bash plugins limitations
  • Plugin Functions
    • Rust plugin dependencies
    • Bash functions arguments
    • Bash function return value
  • Constants
    • Bash
    • Nim
      • Implementation details
      • Using a custom prefix
    • Rust
      • Using a custom class name
  • Persistant state between function calls
    • Rust
    • Bash
• AttrTables
  • Basic concepts
  • Comparison to entity-attribute-value
  • Setup
  • Running the tests suite
  • Usage
• AttrTables: Usage manual
  • Creating the AttributeValueTables instance
    • Computation IDs
    • Value tables
    • Attribute definitions table
  • Creating attributes
    • Datatype description
    • Attribute name reccomendations
  • Setting values of an attribute
    • Setting multiple attributes at once
    • Loading the results of a batch computation
  • Deleting an attribute value
  • Querying the values of an attribute
  • Destroying an attribute
  • Listing the attributes
• SnaCLI
  • Introduction
  • Usage
• Background: Snakemake external Python scripts
• Background: CLI scripts based on docopt
• SnaCLI
  • Mapping of docopt keys to snakemake names
    • Customized docopt key to snakemake name mapping
  • Passing options to docopt
  • Using a script also as a non-interactive module
  • Reusing argument definitions in multiple scripts
    • Multiple entries for the same key