CCPEM-pipeliner

The CCPEM-pipeliner is an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.

The pipeliner brings together a variety of 3rd party software in a single unified framework for seamless integration of the different programs, along with tools for management and analysis of the project.

General info and installation

• README

Getting started

• Getting started

Writing new jobs

• Writing new jobs
• Node type names

Pipeliner API

• CCPEM-Pipeliner API
  • PipelinerProject
  • api_utilities
  • user_settings

Command line tools

• Command Line Tools

Additional tools

• Pipeliner benchmarking tool

Core Modules

• Pipeline Tools
  • Nodes and Processes
  • ProjectGraph
  • Metadata Tools
  • Pipeline Visualisation
• Tools for Running Jobs
  • The JobRunner
  • Check_completion
  • The job factory
• Star File Utilities
  • BodyFile
  • DataStarFile
  • JobStar
  • PipelineStarFile
  • StarFile
  • check_reserved_words()
  • compare_starfiles()
  • get_input_edges()
  • get_nodes()
  • get_output_edges()
  • get_processes()
  • update_nodes_input_to()
  • update_nodes_output_from()
  • update_process_input_edges()
  • Starfile writing utilities
  • write()
  • write_jobstar()
  • write_to_stream()
• General Utilities
  • check_for_illegal_symbols()
  • clean_jobname()
  • date_time_tag()
  • decompose_pipeline_filename()
  • find_common_string()
  • fix_newlines()
  • get_pipeliner_root()
  • make_pretty_header()
  • print_nice_columns()
  • quotate_command_list()
  • run_subprocess()
  • smart_strip_quotes()
  • touch()
  • truncate_number()
  • wrap_text()

Pipeliner jobs and plugins

• Pipeliner Jobs
  • Pipeliner jobs
  • Display tools
  • ResultsDisplay Objects
  • Deposition Objects
  • Deposition tools

• Nodes

• Job Options

• Processes

Indices and tables

• Index

• Module Index

• Search Page