NeatSeq-Flow Monitor

Author: Liron Levin

Affiliation: Bioinformatics Core Facility, National institute of Biotechnology in the Negev, Ben-Gurion University.

: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