kasperskytte/bash_template

A simple BASH template script

BASH_template

A simple BASH template script intended for making convenient scientific workflows in BASH. Includes some helpful functions, for example for printing status messages with a time stamp, checking if required software is available in $PATH, standard argument parsing and help overview, etc. Also writes all output from stderr+stdout streams to a log file as well as the chosen settings. Adjust to your own needs.

Usage

Always include help text and description of arguments:

$ bash template.bash -h
Some help text
Version: 1.2.2
Options:
  -h    Display this help text and exit.
  -v    Print version and exit.
  -i    (required) Input data.
  -o    (required) Output folder.
  -d    (required) Path to database.
  -t    Max number of threads to use. (Default: all available except 2)

Additional options can be set by exporting environment variables before running the script:
  - someinternalvar: Describe the variable

$ bash template.bash -i data/input_file -o data/output -d ../../databases/some_database/database_file
#################################################
Host name: slaptop
Current user name: kapper
System time: 2022-10-03 14:11:27 (Europe/Copenhagen)
Script: /home/kapper/Knockbox/github/BASH_template/template.bash
Script version: 1.2.2 (available at https://github.com/kasperskytte/bash_template)
Current working directory: /home/kapper/Knockbox/github/BASH_template
Input file: /home/kapper/Knockbox/github/BASH_template/data/input_file
Output folder: /home/kapper/Knockbox/github/BASH_template/data/output
Database: /home/kapper/Knockbox/databases/some_database/database_file
Max. number of threads: 10
Log file: /home/kapper/Knockbox/github/BASH_template/data/output/logfile_20221003_141127.txt
#################################################

 *** [2022-10-03 14:11:27] script message: Step 1: I'm gonna sleep for 5 seconds...
 *** [2022-10-03 14:11:32] script message: Step 2: I'm gonna take 2 seconds more...
 *** [2022-10-03 14:11:34] script message: Done. Time elapsed: 00h:00m:07s!

Run it again and it will stop with an error to avoid overwriting output data from a previous run

$ bash template.bash -i data/input_file -o data/output -d ../../databases/some_database/database_file
 *** [2022-08-05 11:29:53] script message: A directory named 'data/output' already exists and is needed for this script to run. Please backup or delete the folder.
 *** [2022-08-05 11:29:53] script message: Exiting script.