Bash process timer

Shell Programming and Scripting
1

I have a bash with several processes in it, that I would like to include a progress bar or percentage complete. Below are two separate processes that, so the user knows that something is happening, there is an an indicator for each process.

Maybe, at the start of each new process a printf the for loop followed by another printf when the process completes. I'm not quite sure if this is the best thing to do. Thank you :).

# create BAM Index
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/*.bam ; do
     bname=`basename $f`
     pref=${bname%%.bam}
     samtools index $f
done

# strip off @PG tags
for f in /home/cmccabe/Desktop/NGS/API/2-12-2015/*.bam ; do
     bname=`basename $f`
     pref=${bname%%.bam}
     samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/API/2-12-2015/${pref}_newheader.bam
done
2

I think you may want bash coprocesses as a starting suggestion.

3

Hi.

Google search progress mechanisms for bash produces about half a million hits, including spinners, bars, etc., and at least one right here need suggestion how to use the progress bar while executing shell ... cheers, drl