for loop with internal unix command in statement throwing error


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# 1  
[Solved] for loop with internal unix command in statement throwing error

Hi

I've gotten a plugin script that won't run. I keeps throwing an error at the following line.

Code:
for BARCODE_LINE in `cat ${TSP_FILEPATH_BARCODE_TXT} | grep "^barcode"`
do
#something
done

The error reads

/results/analysis/output/Home/Auto_KNO-12-Cardiac-panel_27_045/plugin_out/trial_out/ion_plugin_trial_launch.sh: line 146: syntax error near unexpected token `do
'
/results/analysis/output/Home/Auto_KNO-12-Cardiac-panel_27_045/plugin_out/trial_out/ion_plugin_trial_launch.sh: line 146: ` do
'

How can I get this for loop to ignore the backtick? (I tried using a semi-colon at the end of the statement)

Thanks

Last edited by jdilts; 07-06-2012 at 12:34 PM..
# 2  
Can you change it to:
Code:
cat ${TSP_FILEPATH_BARCODE_TXT} | grep "^barcode" | while read BARCODE_LINE
do 
    etc...
done

(no backtick... to see if they are in cause...)
This User Gave Thanks to vbe For This Post:
# 3  
I can reproduce the error in Post #1 by converting the script posted to MSDOS text file format, then executing it.
Was the the script created with a Microsoft Windows editor such as Notepad?

If so, it can be fixed by removing the carriage return characters:
Code:
cat scriptname | tr -d '\r' > newscriptname

This User Gave Thanks to methyl For This Post:
# 4  
Yeah, that was my problem. I did a dos2unix and that fixed it right up.
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