pbsmrtpipe
0.63.0
Site
Installing
How to use pbsmrtpipe
Identifiers Model
Configuration
Tool Contract and Defining Tasks
Tool Contract Unittesting
Constructing Pipelines
Defining Pipeline Templates
Command Line Interface Tools
Job Directory Structure
Pbsmrtpipe TestKit Framework
Pbsmrtpipe Chunking Framework
More Chunking Operators Examples
For task chunking, what do I need to define?
Chunk.json spec
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pbsmrtpipe
Installing »
Source
pbsmrtpipe
¶
Installing
Installing requirements
Running unittests
Running Integration Tests
Running the entire Test Suite
How to use pbsmrtpipe
Getting started
Parallelization
Common workflows
Practical Examples
Appendix A: HdfSubreadSet to SubreadSet conversion
Appendix B: Working with datasets
Identifiers Model
Configuration
Cluster Manager
Environment Handling
Tool Contract and Defining Tasks
Tool Contract Unittesting
Running ToolContract
Constructing Pipelines
Simple Bindings
Basic Task and Bindings Model
Entry Points
Advanced Bindings
Defining Pipeline Templates
Accessing Pipeline Templates by ID
Simple example of running from the Commandline
Explicit Bindings in Pipeline Template
Pipeline Presets
Loading of Presets and the “RC” Preset
Command Line Interface Tools
Core Pbsmrtpipe executable
pbtools-runner
Testkit Runner
Testkit Multi-Runner
Resource RST Pipeline Generation from Resolved Pipeline JSON
Job Directory Structure
Example datastore.json
Task Specific Components
Pbsmrtpipe TestKit Framework
Defining Test Cases
Running Testkit
Pbsmrtpipe Chunking Framework
Chunking Basic Design Model
High level Model of Chunking Steps
Example Chunk model
Chunk Operator for dev_filter_fasta
Step 1.
Step 2.
Step 3.
Step 4.
More Chunking Operators Examples
For task chunking, what do I need to define?
Chunk.json spec