FIX SGEGraph fixed to allow for varied file permissions #1461
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ostanley changed the title 
| @hjmjohnson - can you take a look here? |
| stdoutFile = '-o {outFile}'.format( | ||
| outFile=batchscriptoutfile) | ||
| full_line = '{jobNm}=$(qsub {outFileOption} {errFileOption} {extraQSubArgs} {dependantIndex} -N {jobNm} {batchscript} | awk \'{{print $3}}\')\n'.format( | ||
| full_line = '{jobNm}=$(qsub {outFileOption} {errFileOption} {extraQSubArgs} {dependantIndex} -N {jobNm} bash {batchscript} | awk \'{{print $3}}\')\n'.format( |
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Forgive me if this is an obvious question but how would you do that? You can only use chmod after the file exists and the nipype creates the file just before run. Should I add an os.chmod() command to the script creation?
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By not specifying bash in qsub commands you require the generated files to have executable permissions. Most linux systems create 644 files without these permissions. I corrected this by adding bash to the qsub command before the batchscript variable. If there is another proper way to do this please let me know.
Thank you,
Olivia