In OS X 10.9.5
I wrote a Shell Script (via vim). Save it and navigate to this script and
sh code.shit runs perfect (in iTerm & Total Terminal).
The same command in the same directory produces via Mac Automator always an ERROR. Why?
in Automator and in Terminal.echo $SHELL
/bin/bash
Why is it impossible to run a shellscript via Automator. 
This problem can be solved by adding the following code above your current code:
export PATH=/usr/local/bin:$PATH
I suspect it's the cd Desktop bit. You can try:
(cd ~/Desktop; sh code.sh)
However:
You should make code.sh executable so you don't need to invoke it with sh. This is done with chmod 0755 code.sh.
If you need the shell script to work from a certain directory (i.e. the directory where the script is located) then build that into the script so it can be invoked with just ~/Desktop/code.sh:
#!/bin/bash
dir=$(dirname $0)
cd $dir
# do work
For example:
➜ ~ cat tmp/code.sh
#!/bin/bash
dir=$(dirname $0)
cd $dir
ls -l
➜ ~ chmod 0755 tmp/code.sh
➜ ~ tmp/code.sh
total 64
drwxr-xr-x 6 andy staff 204 Feb 22 18:53 Archives
drwxr-xr-x 11 andy staff 374 Jun 18 13:59 DerivedData
-rw-r--r-- 1 andy staff 225 May 20 13:44 MyFirstProgram.X
-rwxr-xr-x 1 andy staff 3072 May 20 13:44 MyFirstProgram.exe
drwxr-xr-x 3 andy staff 102 Jan 6 2014 bug_reports
-rwxr-xr-x 1 andy staff 43 Aug 6 14:15 code.sh
-rw-r--r-- 1 andy staff 11539 May 20 08:33 iOS_Team_Provisioning_Profile_.mobileprovision
-rw-r--r-- 1 andy staff 1438 May 20 08:40 ios_development.cer
-rwxr-xr-x 1 andy staff 272 Aug 5 08:55 script.sh
Rscript -e 'shiny::runApp(("/Users/Einstein/Git/RShiny/fooapp"),launch.browser=TRUE)' via Terminal, you can see the loading process and the browser opens - perfect. In Automator, no output ...Create two output files:
In Automator:
env > ~/Desktop/file_1.txt
in iTerm:
env > ~/Desktop/file_2.txt
diff -y ~/Desktop/file_1.txt ~/Desktop/file_2.txt
And, voila, there are interessting differences!
Insert the differences e.g. export LANG=de_DE.UTF-8 to the script, and it works!
PATH variable between Automator and Terminal is the main cause of this. Automator defaults to PATH=/usr/bin:/bin:/usr/sbin:/sbin while environmental variable would be similar to PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin so Automator is missing /usr/local/bin. Exporting PATH in Automator script should indeed fix the issue.
code.shexpect some input from somewhere? Can you run it withsh -x(or rather,bash -x, if it's really properly a Bash script) to see where exactly it's failing?can't find lib-x or lib-y. Only STOP. The Shell-script itself contains a RScript.Rscript -e 'shiny::runApp(("/Users/Einstein/Git/RShiny/fooapp"),launch.browser=TRUE)'sleep 1000in the command to run, and press the Stop button after allowing it to run for a while. So I guess that's what you did as well.