Using case in BAtchscript

[vishal.rossi]

Hi,
As I am new to batch and using the case statement for the 1st time, can anyone help me in understanding what is missing in the code below.

Do I need to define "command" before using it in for condition?
Thanks in advance


#!bin/bash -l
## PBS Directives
#PBS -q default
#PBS -l nodes=1pn=4
#PBS -l mem=25GB
#PBS -l walltime=10:00:00
#PBS -A ccg-ngs
#PBS -m abe
#PBS -M ......
#PBS -o /scratch/tmp/v_stdout/${PBS_JOBNAME}.o${PBS_JOBID}
#PBS -e /scratch/tmp/v_stderr/${PBS_JOBNAME}.e${PBS_JOBID}

inp=$input
echo inp:$inp

for command in 1 2 3 4
do
case command in
1)
/path/SVDetect_r0.8/bin/SVDetect linking -conf $inp;;
2)
/path/SVDetect_r0.8/bin/SVDetect filtering -conf $inp;;
3)
/path/SVDetect_r0.8/bin/SVDetect links2circos -conf $inp;;
4)
/path/SVDetect_r0.8/bin/SVDetect links2SV -conf $inp;;
esac
done

[vishal.rossi]

If someone can tell how to execute it with if statements, it will also be fine

[mastal]

Using case in BAtchscript

Do I need to define "command" before using it in for condition?

No, that is fine as it is. But I would beware of using words that
could be actual commands or key words as variable names.

#!bin/bash -l

You should have

#!/bin/bash -l

I'm not sure why you are using the for loop or the case statement.
The way you have written the code, it seems like you just want to
execute 4 commands, one after the other, in which case you just need
to list the commands in the order you want them to be executed.

/path/SVDetect_r0.8/bin/SVDetect linking -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect filtering -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect links2circos -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect links2SV -conf $inp;;

[vishal.rossi]

Thanks for the reply.
I want to execute these 4 commands.
So what you want to say is I simply use this code :


inp=$input
echo inp:$inp
/path/SVDetect_r0.8/bin/SVDetect linking -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect filtering -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect links2circos -conf $inp;;

/path/SVDetect_r0.8/bin/SVDetect links2SV -conf $inp;;

[mastal]

Using case in BAtchscript

T
So what you want to say is I simply use this code :

Yes.

I'm not sure where your scipt is going to get the value of $input from though.

[vishal.rossi]

i will submit a job like this:

qsub -v input=/path/abc.conf /path/svdetect.sh


I tried what you suggested and it throws this error now.
bin/bash: bad interpreter: No such file or directory

[sklages]

bin/bash: bad interpreter: No such file or directory

You surely forgot the '/'. It is /bin/bash