Table of Contents - cagnut_core-0.3.3 Documentation
Classes and Modules
- Cagnut
- Cagnut::Configuration
- Cagnut::Configuration::Base
- Cagnut::Configuration::Checks
- Cagnut::Configuration::Checks::Datasets
- Cagnut::Configuration::Checks::Tools
- Cagnut::JobManage
- Cagnut::NewProject
- Cagnut::Pipeline
- Cagnut::Pipeline::Base
- CagnutCore
Methods
- ::base — Cagnut::Configuration
- ::check_and_load_yml — Cagnut::Configuration
- ::check_datasets — Cagnut::Configuration
- ::check_path — Cagnut::Configuration
- ::config_check — Cagnut::Configuration
- ::configure — Cagnut::Configuration
- ::environment — Cagnut
- ::fetch_system_config_path — Cagnut::Configuration
- ::fetch_tools_config_path — Cagnut::Configuration
- ::load — Cagnut::Configuration::Base
- ::load_config — Cagnut
- ::load_config — Cagnut::Configuration
- ::new — Cagnut::Configuration::Checks::Datasets
- ::new — Cagnut::Configuration::Checks::Tools
- ::params — Cagnut::Configuration
- ::prefix_name — Cagnut
- ::register — Cagnut::Pipeline::Base
- ::root — Cagnut
- ::run_local — Cagnut::JobManage
- ::submit — Cagnut::JobManage
- ::tools_check — Cagnut::Configuration
- #add_queue_setting — Cagnut::NewProject
- #after_new_project — Cagnut::NewProject
- #append_pipeline_dependency_gems_to_gemfile — Cagnut::NewProject
- #append_pipeline_gems_to_gemfile — Cagnut::NewProject
- #attributes — Cagnut::Configuration::Base
- #bundle — Cagnut::NewProject
- #check — Cagnut::Configuration::Checks::Datasets
- #check — Cagnut::Configuration::Checks::Tools
- #check_datatype — Cagnut::Configuration::Checks::Datasets
- #check_each_tool — Cagnut::Configuration::Checks::Tools
- #check_execute_system — Cagnut::Configuration::Checks::Tools
- #check_file_size — Cagnut::Configuration::Checks::Datasets
- #check_java — Cagnut::Configuration::Checks::Tools
- #check_ln_file — Cagnut::Configuration::Checks::Datasets
- #check_pipeline — Cagnut::NewProject
- #check_pu — Cagnut::Configuration::Checks::Datasets
- #check_r — Cagnut::Configuration::Checks::Tools
- #check_r_libs — Cagnut::Configuration::Checks::Tools
- #check_ref_fasta — Cagnut::Configuration::Checks::Tools
- #check_tool — Cagnut::Configuration::Checks::Tools
- #check_tool_ver — Cagnut::Configuration::Checks::Tools
- #create_analysis_folder — Cagnut::Configuration::Checks::Datasets
- #dir_present? — Cagnut::Configuration::Checks::Datasets
- #dir_rm_slash — Cagnut::Configuration::Checks::Datasets
- #execute_command — Cagnut::Pipeline::Base
- #export_command — Cagnut::JobManage
- #fetch_flist — Cagnut::Configuration::Checks::Datasets
- #fetch_seqs — Cagnut::Configuration::Checks::Datasets
- #files_to_much? — Cagnut::Configuration::Checks::Datasets
- #full_command — Cagnut::JobManage
- #generate_pipeline_tools_config — Cagnut::NewProject
- #get_config_name — Cagnut::Pipeline::Base
- #link_name — Cagnut::Configuration::Checks::Datasets
- #ln_fastq_file — Cagnut::Configuration::Checks::Datasets
- #ln_seq_files — Cagnut::Configuration::Checks::Datasets
- #ln_seq_files_to_folder — Cagnut::Configuration::Checks::Datasets
- #ln_seq_txt_file — Cagnut::Configuration::Checks::Datasets
- #load — Cagnut::Configuration::Base
- #load_bundle_env — Cagnut::NewProject
- #local — Cagnut::JobManage
- #make_required_folders — Cagnut::Configuration::Checks::Datasets
- #new — Cagnut::NewProject
- #new_project — Cagnut::NewProject
- #pepeline_opts — Cagnut::Pipeline::Base
- #project_opts — Cagnut::NewProject
- #run_filter — Cagnut::Pipeline::Base
- #run_local — Cagnut::JobManage
- #run_local? — Cagnut::JobManage
- #run_pipeline — Cagnut::Pipeline::Base
- #setup_requirements — Cagnut::Configuration::Checks::Datasets
- #start — Cagnut::Pipeline::Base
- #submit — Cagnut::JobManage
- #wait_local — Cagnut::JobManage