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Read Parameters from one file and make a script

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# 1  
Old 07-22-2013
Read Parameters from one file and make a script
Hi Friends,

I have the following input parameters file

Code:
name
input
err1
out1
1
40G
DET
sylamer
dir1
dir2
123456

I want to make the following script

Code:
#!/bin/bash
#
# Name: name
# Task: name
#
#$ -N name
#$ -e input/err1.log
#$ -o input/out1.log
#$ -pe threaded 1
#$ -l h_vmem=40G

LD_LIBRARY_PATH="/usr/lib64/"

export LD_LIBRARY_PATH

cd input

mkdir input/DET/

mkdir input/sylamer/

mkdir input/DET/dir1_vs_dir2

mkdir input/sylamer/dir1_vs_dir2

myprogram.sh -i 123456 -o input/DET/dir1_vs_dir2 -1 input/dir1 -2 input/dir2

cd input/sylamer/dir1_vs_dir2

R CMD BATCH --no-save --no-restore "--args ref=\"mmu\" DETDIR=\"input/DET/dir1_vs_dir2\" outName=\"dir1_vs_dir2\" UCSCLink=\"http://test.com?id=123456\"" myprogram2.sh

So, the order of parameters u see in the input file are coming in the same order in the output too. Please don't hesitate to reply if you have any questions or suggestions on how to deal with. Thanks in advance.
# 2  
Old 07-22-2013
I'm sure I don't understand your request. The nearest guess I have is: you have a skeleton script with some placeholders that you then fill in/replace with data from another file. That you could do with an awk script... read in the data, and then read & edit the skeleton script.
# 3  
Old 07-22-2013
Quote:
Originally Posted by RudiC
I'm sure I don't understand your request. The nearest guess I have is: you have a skeleton script with some placeholders that you then fill in/replace with data from another file. That you could do with an awk script... read in the data, and then read & edit the skeleton script.
@Rudic, thanks for the response.

Your guess is right. I have my input and I want to make the output script by placing the input content at certain places. But, I have never done such complex replacement tasks. Any other starting points?
# 4  
Old 07-26-2013
I'm not sure that modifying a script is a good choice. Why don't you make your parameter file a variable definition file like
Code:
var1=name
var2=input
var3=err1
... etc.

, source it in your script and put the respective variables at the respective places:
Code:
mkdir $var2/$var7

?
# 5  
Old 07-27-2013
If you're always going to expect the same order/variables/naming conventions/etc you can extract the properties of your configuration file easy enough with grep & awk. You could probably use just awk, but, here's the easiest way.

Code:
#properties.prop
CDDIR::input

-----------
#Script
PROP_CDDIR=$(grep CDDIR properties.prop | awk"::" '{print $2}')
cd $PROP_CDDIR

Allows a person to do some very interesting dynamic coding. Smilie
# 6  
Old 07-27-2013
check this.. if it ok for you.

Code:
i=1
while read line
do

	var$i=$line
	i=`expr $i + 1`

done < inputfile.txt
echo "==========================="
echo "creating the shell script"
echo "==========================="

echo "#!/bin/bash" > shellscript.sh
echo "#" >> shellscript.sh
echo "# Name: $var1" >> shellscript.sh
echo "# Task: $var1" >> shellscript.sh
echo "#" >> shellscript.sh
echo "#$ -N $var1"	>> shellscript.sh			
echo "#$ -e $var2/$var3.log"	>> shellscript.sh				
echo "#$ -o $var2/$var4.log"	>> shellscript.sh				
echo "#$ -pe threaded $var5"	>> shellscript.sh		
echo "#$ -l h_vmem=$var6"	>> shellscript.sh		
echo "" >> shellscript.sh
echo "LD_LIBRARY_PATH="/usr/lib64/" >> shellscript.sh
echo ""  >> shellscript.sh
echo "export LD_LIBRARY_PATH" >> shellscript.sh
echo ""  >> shellscript.sh
echo "cd $var2"	>> shellscript.sh		
echo ""   >> shellscript.sh
echo "mkdir $var2/$var7/"	>> shellscript.sh		
echo ""  >> shellscript.sh
echo "mkdir $var2/$var8/"  >> shellscript.sh			
echo ""  >> shellscript.sh
echo "mkdir $var2/$var7/$var9_vs_$var10"  >> shellscript.sh	
echo ""  >> shellscript.sh
echo "mkdir $var2/$var8/$var9_vs_$var10" >> shellscript.sh	
echo ""  >> shellscript.sh
echo "myprogram.sh -i $var11 -o $var2/$var7/$var9_vs_$var10 -$var5 $var2/$var9 -2 $var2/$var10" >> shellscript.sh   
echo ""  >> shellscript.sh
echo "cd $var2/$var8/$var9_vs_$var10"  >> shellscript.sh		
echo ""   >> shellscript.sh
echo "R CMD BATCH --no-save --no-restore "--args ref=\"mmu\" $var7DIR=\"$var2/$var7/$var9_vs_$var10\" outName=\"$var9_vs_$var10\" UCSCLink=\"http://test.com?id=$var11\"" myprogram2.sh >> shellscript.sh


you script that will be created is shellscript.sh
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