NeatSeq-Flow Monitor

Author: Liron Levin

Table of Contents

:Neatseq-Flow Monitor

:Neatseq-Flow Monitor 

Authors: Liron Levin
Affiliation: Bioinformatics core facility
Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.

SHORT DESCRIPTION 

Neatseq-Flow Monitor can be used to track the progress of running work-flows of a specific project in real-time.

Alternatively Neatseq-Flow Monitor can be used to compare between previous runs of a specific project.

Neatseq-Flow Monitor uses the information in the Neatseq-Flow log files and information gathered from the cluster scheduler

Neatseq-Flow monitor provides the following information:

List of available log files for a specific work-flow [project]

List of steps and samples as they distribute by the cluster scheduler

Steps and samples Start and finished times

Number of started and finished jobs

Number and identity of the current ruining jobs

Step progress bar

Color indication for the status of steps and samples

Requires 

Neatseq-Flow Monitor is written in python and requires the following packages that are not included in python 2.7 release:

pandas

Parameters that can be set 

Parameter	Values	Comments
-D	PATH	Neatseq-flow project directory [default= current working directory ]
-R	STR	Log file Regular Expression [in ./log/ ] [default=log_[0-9]+.txt$]
–Monitor_RF	FLOAT	Monitor Refresh rate [default=1]
–File_browser_RF	FLOAT	File Browser Refresh rate [default=1]
–Bar_Marker	CHAR	Progress Bar Marker [default=#]
–Bar_Spacer	CHAR	Progress Bar Spacer [default=Space]
–Bar_len	INT	Progress Bar Total Length [in chars] [default=50]

Comments 

Note

Neatseq Flow Monitor can be run only after the Neatseq Flow script generator is finished successfully [a project is created]

Tip

Running neatseq_flow_monitor.py from the project directory without arguments will use all the default parameters and will show the project available log files.

Help message:

usage: Neatseq_Flow_Monitor.py  [-h] [-D STR] [-R STR] [--Monitor_RF FLOAT]
                                [--File_browser_RF FLOAT]
                                [--Bar_Marker CHAR] [--Bar_Spacer CHAR]
                                [--Bar_len INT]

Neatseq-flow Monitor_v1.1 By Liron Levin

optional arguments:
  -h, --help                show this help message and exit
  -D STR                    Neatseq-flow project directory [default=cwd]
  -R STR                    Log file Regular Expression [in ./log/ ]
                            [default=log_[0-9]+.txt$]
  --Monitor_RF FLOAT        Monitor Refresh rate [default=1]
  --File_browser_RF FLOAT
                            File Browser Refresh rate [default=1]
  --Bar_Marker CHAR         Progress Bar Marker [default=#]
  --Bar_Spacer CHAR         Progress Bar Spacer [default=Space]
  --Bar_len INT             Progress Bar Total Length [in chars] [default=50]

NeatSeq-Flow Monitor