Shell Programming and Scripting

Hello,
I know this is a situation about the single quote and double literal, but I could not figure out after many search.

I need to loop through thousands of different BACs sequencing to optimize kmer individually.

Code:

IN=/PATH/TO/INPUT/FILES
for sample in S{01..1096}
do
     run_program in='$IN/${sample}_file1.fa $IN/${sample}_file2.fa' 
done

The package asks

Code:

in='input_file1 input_file2'

for the input files. Because of the single quote in the command option, the embedded shell variables cannot be interpreted literally. Is there a way to handle this situation?

Thanks a lot!

Yifang

Code:

[user@host ~]$ x=2
[user@host ~]$ echo '$x'
$x
[user@host ~]$ echo "$x"
2
[user@host ~]$

HTH

Yes, I am aware of the difference. The problem I met is the $x should be changed each loop, but the single quote of the command parameter escaped the $ sign of $x. Maybe I should ask like this:

Code:

MYVAR=sometext 
echo 'single quotes gives you $MYVAR'

Is there away to get output from the single quotes expression as the double quoted one? i.e.

Code:

echo 'single quotes gives you $MYVAR'
Output: 
single quotes gives you sometext

I cannot change the single quote as it has been set by the package. Thanks again!

Thanks!
The awk examples seems a possible way to what I want, but not exactly. It seems there is no way to change the single quote literal in bash for my case. I thought there could be a way to get what I want. Waiting for more ideas.
Thanks a lot in advance!

Well, what can you change? The easiest solution is:

Code:

run_program in="$IN/${sample}_file1.fa $IN/${sample}_file2.fa"

Ah, how simple it is!!! It works now.
Does this replacement apply to all the case IF there is embedded variable inside the single quote in general? I mean generally.
Thanks a lot again!