The pipeline will use default unix behavior for setting permissions on the files it creates (i.e. based on user's umask and default group or inherit the directory group if the setgid bit is set). Per best practices where files should be default be editable by everyone in genetics to enable collaboration but not accessible to anyone outside genetics, perhaps the qsub_Rcall.sh script should do a recursive chgrp / chmod after the R call to give edit access to everyone in gxpipe and remove all access from those outside the group.
The pipeline will use default unix behavior for setting permissions on the files it creates (i.e. based on user's umask and default group or inherit the directory group if the setgid bit is set). Per best practices where files should be default be editable by everyone in genetics to enable collaboration but not accessible to anyone outside genetics, perhaps the qsub_Rcall.sh script should do a recursive chgrp / chmod after the R call to give edit access to everyone in gxpipe and remove all access from those outside the group.