rsync fails if experiment name contains a space

CarragherLab / cptools2

Running cellprofiler on eddie3 / SGE clusters

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rsync fails if experiment name contains a space #16

Closed Swarchal closed 6 years ago

Swarchal commented 6 years ago

Got it working by using rsync's -s flag and placing quotes around filenames, though only works outside of cptools2.

No idea why it's breaking when ran from a qsub script.

Swarchal commented 6 years ago

One bodge is to save individual rsync commands as temporary files and run them.

SEEDFILE="/home/s1027820/nuclei_annotated/staging.txt"    
SEED=$(awk "NR==$SGE_TASK_ID" "$SEEDFILE")                

echo "$SEED" > rsync_command_"$SGE_TASK_ID".sh            
bash rsync_command_"$SGE_TASK_ID".sh                      
rm rsync_command_"$SGE_TASK_ID".sh

But it's a horrible hack.