HIPPIE User Manual v0 1 2014 5 18 Yih Chii Hwang yihhwang at mail med upenn edu OVERVIEW OF HIPPIE O Flowchart of HIPPIE O Requirements o Directory structure for HIPPIE execution CREATE THE CONFIGURATION FILE PREPARE THE REFERENCE GENOME RUN HIPPIE THE PHASE MODE PIPELINE EXECUTION THE TASK MODE RERUNNING SELECTED PORTIONS OF THE PIPELINE THE DEBUG MODE DEBUGGING OPTION PHASES AND TASKS o Phase1 Read Mapping Phase2 Quality Control Phase3 Peak identific
HIPPIE User Manual vO 1c 2014 9 29 Yih Chii Hwang yihhwang at mail med upenn edu e OVERVIEW OF HIPPIE o Flowchart of HIPPIE O Requirements o Directory structure for HIPPIE execution CREATE THE CONFIGURATION FILE PREPARE THE REFERENCE GENOME INSTALL MATH CDF PERL PACKAGE RUN HIPPIE THE PHASE MODE PIPELINE EXECUTION THE TASK MODE RERUNNING SELECTED PORTIONS OF THE PIPELINE THE DEBUG MODE DEBUGGING OPTION PHASES AND TASKS o Phasei Read Mapping Phase2 Quality
HIPPIE User Manual vO 0 2 beta 2015 4 26 Yih Chii Hwang yihhwang at mail med upenn edu OVERVIEW OF HIPPIE o Flowchart of HIPPIE o Requirements PREPARE DIRECTORY STRUCTURE FOR HIPPIE EXECUTION o Library sample directory and expected input fastq filename format o Log directory SHOME hippie stdout CREATE CONFIGURATION FILE PREPARE THE REFERENCE GENOME INSTALL PYSAM PYTHON PACKAGE INSTALL MATH CDF PERL PACKAGE RUN HIPPIE THE PHASE MODE PIPELINE EXECUTION THE