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
Getting started
Writing new jobs
Pipeliner API
Command line tools
Core Modules
- Pipeline Tools
- Tools for Running Jobs
- Star File Utilities
BodyFileDataStarFileJobStarPipelineStarFileStarFilecheck_reserved_words()compare_starfiles()get_input_edges()get_nodes()get_output_edges()get_processes()interconvert_box_star_coords()update_nodes_input_to()update_nodes_output_from()update_process_input_edges()- Starfile writing utilities
write()write_jobstar()write_to_stream()
- General Utilities
DirectoryBasedLockcheck_for_illegal_symbols()clean_job_dirname()clean_jobname()compare_nested_lists()convert_relative_filename()count_file_lines()date_time_tag()decompose_pipeline_filename()file_in_project()find_common_string()format_strings_to_numbers()get_file_size()get_job_number()get_job_runner_command()get_job_script()get_pipeliner_root()get_python_command()is_uuid4()launch_detached_process()make_pretty_header()print_nice_columns()run_subprocess()smart_strip_quotes()str_is_hex_colour()subprocess_popen()touch()truncate_number()wrap_text()