I want to automate a process, done by a specific software. I want software do this job in the respective directories. I have some 94 directories and each directory have the respective files on which calculation needs to be done. The script that I wrote, call another file(autodock) containing instructions for specific action made on the files. But the my script not working properly.It is not changing the directory (cd command with the variable)
Here is my script:

#!/bin/bash
#this scrip automate the docking process
for DIR in `ls -ltr | awk '/^d/' | awk '{print $8}'`
do
cd ${DIR}
./autodock
done


the error is:
mazingaz:/home/puneet/Desktop/test_dock> ./ready
./ready: line 6: ./autodock: No such file or directory
./ready: line 5: cd: 2QZK: No such file or directory
./ready: line 6: ./autodock: No such file or directory

The variable seems to be working properly but why the cd is not working..far from my understanding

Please suggest


Thanks

You have to use absolute path, either for the script ./autodock and for the directories. If you cd into one directory, you cannot change to another directory in the list if you don't go back into the previous one. And if you launch autodock from each directory a copy of it should be inside all of them. Here is a solution:

I would put something like
cd ..
before "done".

I mean, you got into a directory, you should get out before entering another one.

It should not be enough if the directory listing includes multiple levels of the subdirectories tree. Eventually
could do the trick.

If the OP wants multiple levels, his simple loop will not work anyway. He'll need a recursion. With a single list of dirs returned by his command, there's just one level.

Correct. I confused -r with -R. Sorry.

yeah..

with cd .. it is working perfectly..

thanks a lot

And do you have the script inside every directory???

yes a copy of autodock script i have in each directory..