When I run this command in the bash terminal it works:
awk '{ sum += $1 } END { print sum }' /user/dnaiel/test.txt > /user/dnaiel/sum.txt
But when I run this:
bsub -q priority -R'rusage[mem=2000]' -oo bin${count}.out -eo bin${count}.err \
"awk '{ sum += $1 } END { print sum }' /user/dnaiel/test.txt > /user/dnaiel/sum.txt"
It does not work. I also tried changing ' to \' but also does not work.
I get the following errors: for the first case:
awk: { sum += } END { print sum }
awk: ^ syntax error
for the case I used \'
awk: '{
awk: ^ invalid char ''' in expression
Any ideas where I am messing up with the syntax? I am quite puzzled.
Thanks
notice how the $1 has disappeared in the error message?
awk: { sum += } END { print sum }
awk: ^ syntax error
This is because in shell, when you quote something FIRST with dbl-quotes, as you have done with
bsub -q priority -R'rusage[mem=2000]' -oo bin${count}.out -eo bin${count}.err \
"awk '{ sum += $1 } END { print sum }' /user/dnaiel/test.txt > /user/dnaiel/sum.txt"
any ${var} references are expanded to their value. The single-quotes have lost their magic power to prevent variable expansion when they are inside a dbl-quoted string.
How to fix, escape your $s. not sure what bsub is, but this should do it:
bsub -q priority -R'rusage[mem=2000]' -oo bin${count}.out -eo bin${count}.err \
"awk '{ sum += \$1 } END { print sum }' /user/dnaiel/test.txt > /user/dnaiel/sum.txt"
# -------------^^^
IHTH