Method List
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#attributes Cagnut::Configuration::Base
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base Cagnut::Configuration
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#check Cagnut::Configuration::Checks::Tools
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#check Cagnut::Configuration::Checks::Datasets
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#check_completed Cagnut::Configuration::Checks::Tools
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#check_datatype Cagnut::Configuration::Checks::Datasets
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#check_each_tool Cagnut::Configuration::Checks::Tools
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#check_execute_system Cagnut::Configuration::Checks::Tools
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#check_file_size Cagnut::Configuration::Checks::Datasets
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#check_java Cagnut::Configuration::Checks::Tools
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#check_ln_file Cagnut::Configuration::Checks::Datasets
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#check_pu Cagnut::Configuration::Checks::Datasets
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#check_r Cagnut::Configuration::Checks::Tools
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#check_r_libs Cagnut::Configuration::Checks::Tools
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#check_ref_fasta Cagnut::Configuration::Checks::Tools
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#check_tool Cagnut::Configuration::Checks::Tools
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#check_tool_ver Cagnut::Configuration::Checks::Tools
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#cluster Cagnut::Configuration::Base
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#config Cagnut::Configuration::Checks::Tools
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#config Cagnut::Configuration::Checks::Datasets
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configure Cagnut::Configuration
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#create_analysis_folder Cagnut::Configuration::Checks::Datasets
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#data_type Cagnut::Configuration::Base
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#dbsnp_ref_indels Cagnut::Configuration::Base
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#dir_present? Cagnut::Configuration::Checks::Datasets
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#dir_rm_slash Cagnut::Configuration::Checks::Datasets
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#dodebug Cagnut::Configuration::Base
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environment Cagnut
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#export_command Cagnut::JobManage
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#fetch_flist Cagnut::Configuration::Checks::Datasets
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#fetch_seqs Cagnut::Configuration::Checks::Datasets
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#files_to_much? Cagnut::Configuration::Checks::Datasets
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#full_command Cagnut::JobManage
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#initialize Cagnut::Configuration::Checks::Tools
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#initialize Cagnut::Configuration::Checks::Datasets
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#java Cagnut::Configuration::Checks::Tools
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#java_path Cagnut::Configuration::Base
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#jobs_dir Cagnut::Configuration::Base
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#link_name Cagnut::Configuration::Checks::Datasets
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#ln_fastq_file Cagnut::Configuration::Checks::Datasets
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#ln_seq_files Cagnut::Configuration::Checks::Datasets
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#ln_seq_files_to_folder Cagnut::Configuration::Checks::Datasets
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#ln_seq_txt_file Cagnut::Configuration::Checks::Datasets
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#load Cagnut::Configuration::Base
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load Cagnut::Configuration::Base
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load_config Cagnut::Configuration
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load_config Cagnut
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#local Cagnut::JobManage
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#magic28 Cagnut::Configuration::Base
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#make_required_folders Cagnut::Configuration::Checks::Datasets
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#new Cagnut::NewProject
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params Cagnut::Configuration
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#pipeline_name Cagnut::Configuration::Base
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pipelines Cagnut::Pipeline::Base
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#prefix_name Cagnut::Configuration::Base
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prefix_name Cagnut
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#ref_fasta Cagnut::Configuration::Base
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register Cagnut::Pipeline::Base
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root Cagnut
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#run_local Cagnut::JobManage
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run_local Cagnut::JobManage
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#run_local? Cagnut::JobManage
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#sample_name Cagnut::Configuration::Base
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#seqs_path Cagnut::Configuration::Base
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#setup_requirements Cagnut::Configuration::Checks::Datasets
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#snpdb Cagnut::Configuration::Base
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#start Cagnut::Pipeline::Base
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#submit Cagnut::JobManage
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submit Cagnut::JobManage
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#target Cagnut::Configuration::Base
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#target_flanks_file Cagnut::Configuration::Base
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#wait_local Cagnut::JobManage