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Full Discussion: How to insert a string and variable at specified position in command in bash?
Top Forums UNIX for Beginners Questions & Answers How to insert a string and variable at specified position in command in bash? Post 303042141 by rbatte1 on Monday 16th of December 2019 09:55:13 AM
Old 12-16-2019
Do you want something more like:
Code:
printf -- "/path/to/xxx.py \\\\\n%s\n\t--ref /path/to/file \\\\\n\t--run /path/to/data\n" \                       # Set up the output format with fixed strings and an assignment for where the data goes
   "$(for bamfile in *.bam; do printf -- "\t\t--bam %s \\\\\n"    "${bamfile}"; done)"                            # Collect & list the data file lines here, tab indenting each with \t and finishing with the formatting to append the \ and the new-line
                                                                                                                  # This will get used in the above line as the input for the data.

Lots of escaping in the strings which makes it look a bit messy, but it seems to work for me. After creating dummy files as you have, I got the output:-
Code:
/path/to/xxx.py \
		--bam s1.bam \
		--bam s2.bam \
		--bam s3.bam \
		--bam s4.bam \
	--ref /path/to/file \
	--run /path/to/data

Does this do what you need?


Robin
Last edited by rbatte1; 12-17-2019 at 07:07 AM..
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bam

BAM(1)								   User Commands							    BAM(1)

NAME

       bam - fast and flexible build system

SYNOPSIS

       bam [OPTION]... [VARIABLE=VALUE]... [TARGET]...

DESCRIPTION

       Builds applications using the bam build system.

	      Execution:

       -a     abort on error

       -c     clean targets

       -d     build targets that is dependent given targets

       --dry  dry run, don't run any jobs

       -j     sets the number of threads to use (default: 0, disabled)

       -s     bam file to use (default: bam.lua)

	      Lua:

       -l     print local variables in backtrace

       -t     print backtrace when an error occurs

	      Output:

       -r     build progress report format (default: s) b = progress bar c = use ansi colors s = build steps

       -v     be verbose

	      Other:

       -n     don't use cache

       -h, --help
	      prints this help

	      Debug:

       --debug-nodes
	      prints all the nodes with dependencies

       --debug-detail
	      prints all the nodes with dependencies and details

       --debug-jobs
	      prints all the jobs that exist

       --debug-dot
	      prints all nodes as a graphviz dot file

       --debug-jobs-dot
	      prints all jobs as a graphviz dot file

       --debug-trace-vm
	      prints a line for every instruction the vm makes

       --debug-dump-int
	      prints the internals scripts to stdout

       --debug-no-int
	      don't load internal scripts

       bam by Magnus Auvinen (magnus.auvinen@gmail.com)

bam								     May 2011								    BAM(1)
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