Removing the quotes and adding the escape before the first $ as you
suggested fixed the error. I see what was happening now.
infile=\$(awk -v line=\$SGE_TASK_ID 'NR == line' /myPath/
my_outfile_list.txt)
I really appreciate your help figuring this out!
Thanks,
Sara
On Apr 17, 2012, at 8:14 AM, Reuti wrote:
Am 17.04.2012 um 16:58 schrieb Sara Rolfe:
Thanks, I did try single quotes too, but get the same problem.
Maybe it would help if you could look at the test script I'm
submitting? I'd really like to know if there's something I'm doing
which makes escaping the variables necessary. I've copied it below.
#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#
start=1
end=3
step=1
email="[email protected]"
jobname="SmoothingFilter_test"
#
cat <<EOF | qsub
No cat necessary:
qsub <<EOF
#!/bin/bash
#\$ -S /bin/bash
#\$ -M $email
#\$ -m be
#\$ -N $jobname
#\$ -t $start-$end:$step
#\$ -e /myPath
#\$ -o /myPath
No \ necessary, as $ followed by a blank won't be expanded.
Why not specifying all as arguments to the `qsub` command itself?
#
uname -a
#
infile=$(awk -v 'line=$SGE_TASK_ID' 'NR == line' /myPath/
my_outfile_list.txt)
infile=\$(awk -v line=\$SGE_TASK_ID 'NR == line' /myPath/
my_outfile_list.txt)
It should be expanded at execution time, not while the script is
created. So the $ needs to be escaped in both locations, and later
on no ', as it would prohibit the expansion.
The below mentioned:
awk "NR==\$SGE_TASK_ID" /myPath/fileList.txt
should work too
-- Reuti
#
echo "The input file is: $infile"
echo "The escaped input file is: \$infile"
echo "The task ID is: $SGE_TASK_ID"
echo "The escaped task ID is: \$SGE_TASK_ID"
#
EOF
#
exit 0
The output file for the third iteration is:
The input file is:
The escaped input file is:
The task ID is: undefined
The escaped task ID is: 3
On Apr 17, 2012, at 2:37 AM, Reuti wrote:
Am 17.04.2012 um 11:08 schrieb George Georgalis:
On Mon, Apr 16, 2012 at 10:37 PM, Sara Rolfe <[email protected]
> wrote:
I am new to both scripting and SGE, so I don't understand why,
but I need to
escape all the variables in my script. For example,
awk "NR==$SGE_TASK_ID" /myPath/fileList.txt
produces a blank output, but if I escape the env variable, like:
awk "NR==\$SGE_TASK_ID" /myPath/fileList.txt
then I get the correct line from the text file. The problem is
when I try
to assign this output to a variable. I still need to use the
escape, but I
think it's not being passed correctly.
I usually use single quotes for awk. It prevents shell expansion of
the symbols. (Shell expansion applies to double quoted arguments
but
not single quoted ones.)
I second this. Using -v to pass arguments to awk (they are known
in the BEGIN block already) or list them after the script (they
are only available outside of the BEGIN block) and using single
quotation marks for the script is the careful way to avoid the
mentioned side effects.
But I would accept an exception here if the only rule is a test
for the NR field as it's still clear what is done.
--
Do you submit an array job? Otherwise $SGE_TASK_ID won't be set to
1 but "undefined". Then:
${SGE_TASK_ID/undefinded/1}
might help and give you a 1 for non-array jobs, hence:
#!/bin/sh
echo $(awk "NR==${SGE_TASK_ID/undefined/1}" file)
is working fine for me.
-- Reuti
.George
--
George Georgalis, (415) 894-2710, http://www.galis.org/
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