Running a shell script from Java returning "command not found"

Question

I've created a java GUI using NetBeans v.8.2. Very new to Java.

One of the buttons in the GUI launches a shell script (I am aware that this is not ideal Java practice, but it is appropriate for my use case) using arguments gathered from other buttons/text fields in the GUI:

    ```
        private void RunMacActionPerformed(java.awt.event.ActionEvent evt) {                                       
            String command[] = {scriptDirStr + "/./Master_run.sh",
                                projDirStr+"/",
                                DestDirStr+"/",
                                ECnonNormStr,
                                ECnormStr,
                                ProjID.getText(),
                                scriptDirStr +"/"};
            System.out.print(Arrays.toString(command));
            ProcessBuilder pb = new ProcessBuilder(command);
            try {
                Process p = pb.start();
            } catch (IOException ex) {
                Logger.getLogger(NewJFrame.class.getName()).log(Level.SEVERE, null, ex);
            }
        }                                      
    ```

So, the idea is to launch Master_run.sh with a bunch of arguments. Master_run.sh runs other R and python scripts, e.g.:

python2 $script_Path/array_data_extractor.py $spath >>$spath/masterOutput.txt 2>>$spath/masterErrors.txt

and

Rscript $script_Path/1_APS_generator_master.R $spath $dpath $APS_src_filename $project_ID $APS_norm_src_filename >>$spath/masterOutput.txt 2>>$spath/masterErrors.txt

and ends with

cat $spath/masterErrors.txt| mail -s $Project_title" done" [email protected]

I know the script gets launched because I get an email with the following errors:

"...line 14: python2: command not found"

and

"...line 16: Rscript: command not found"

When I run Master_run.sh with the same exact arguments from within the terminal, there are no such errors. Does anybody know what might be going wrong and/or how to fix it?

To rephrase the problem, it seems I am getting different behavior launching the same commands from within java vs. directly onto the command line.

glenn jackman · Accepted Answer · 2016-11-16 17:47:26Z

2

Your shell environment is clearly different from java's environment. Try specifying the full path to python2 and Rscript. For example

/usr/local/bin/python2 $script_Path/array_data_extractor.py ...

answered Nov 16, 2016 at 17:47

glenn jackman

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1 Comment

Atticus29 Over a year ago

Could sourcing my .bash_profile from within the script do the trick?

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