agave-jobs/jobs-core/src/main/java/org/iplantc/service/jobs/managers/launchers/CondorLauncher.java
/**
	 * This method will write the generic transfer_wrapper.sh file that condor_submit
	 * uses as it's executable. The file wraps the defined executable for the job along
	 * with the data all tar'd and zipped to transfer to OSG
     *
     * @return the content of the condor transfer_wrapper.sh script
     * @throws JobException if unable to write or set permissions on template and executable files.
	 */
This method will write the generic transfer_wrapper.sh file that condor_submit
uses as it's executable. The file wraps the defined executable for the job along
with the data all tar'd and zipped to transfer to OSG

@return the content of the condor transfer_wrapper.sh script
@throws JobException if unable to write or set permissions on template and executable files.
This method will write the generic transfer_wrapper . sh file that condor_submit uses as it ' s executable . The file wraps the defined executable for the job along with the data all tar ' d and zipped to transfer to OSG @return the content of the condor transfer_wrapper . sh script @throws JobException if unable to write or set permissions on template and executable files .
private String createTransferWrapper() throws JobException {
	    step = "Creating Condor submission transfer wrapper to run " + 
	            getJob().getSoftwareName() + " for job " + getJob().getUuid();
	    log.debug(step);
        String executablePath = getExecutablePath();
        return "#!/bin/bash" +
                "\n\n" +
                "tar xzvf transfer.tar.gz" +
                "\n" +
                "# we supply the executable and path from the software definition" +
                "\n" +
                String.format("./%s # this in turn wraps the final executable along with inputs, parameters and output.\n", executablePath);
             need to make sure that transfer_wrapper.sh is executable
            Files.setPosixFilePermissions(getTempAppDir().toPath().resolve("transfer_wrapper.sh"),
                    PosixFilePermissions.fromString("rwxr-x---"));
            Files.setPosixFilePermissions(getTempAppDir().toPath().resolve(executablePath),
                    PosixFilePermissions.fromString("rwxr-x---"));
	    } catch (IOException e) {
	        String msg = "Failure to write transfer script for Condor submission to " + getTempAppDir() + ".";
	        log.error(msg, e);
	        throw new JobException(msg, e);
	    }
	}
private String createTransferWrapper ( ) throws JobException { step = "Creating Condor submission transfer wrapper to run " + getJob ( ) . getSoftwareName ( ) + " for job " + getJob ( ) . getUuid ( ) ; log . debug ( step ) ; String executablePath = getExecutablePath ( ) ; return "#!/bin/bash" + "\n\n" + "tar xzvf transfer.tar.gz" + "\n" + "# we supply the executable and path from the software definition" + "\n" + String . format ( "./%s # this in turn wraps the final executable along with inputs, parameters and output.\n" , executablePath ) ; }
This method will write the generic transfer_wrapper.sh file that condor_submit
 uses as it's executable.
This method will write the generic transfer_wrapper . sh file that condor_submit uses as it ' s executable .
//        try(FileWriter transferWriter = new FileWriter(getTempAppDir() + File.separator + "transfer_wrapper.sh");) { //	    try { //transferScript.append("chmod u+x " + executablePath + " \n"); // write the transfer_wrapper.sh file //	        transferWriter.write(transferScript.toString()); //	        transferWriter.flush(); // //            // need to make sure that transfer_wrapper.sh is executable //            Files.setPosixFilePermissions(getTempAppDir().toPath().resolve("transfer_wrapper.sh"), //                    PosixFilePermissions.fromString("rwxr-x---")); // //            Files.setPosixFilePermissions(getTempAppDir().toPath().resolve(executablePath), //                    PosixFilePermissions.fromString("rwxr-x---")); //	    } catch (IOException e) { //	        String msg = "Failure to write transfer script for Condor submission to " + getTempAppDir() + "."; //	        log.error(msg, e); //	        throw new JobException(msg, e); //	    }