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BF: Fix for gpu-submission when using the fsl_sub shell plugin

Matthew Webster requested to merge bf/shellgpusubmit into master

Currently the xtract script will fail when submitting a gpu-task via the new fsl_sub shell plugin ( this isn't an issue for cluster-based submission, hence not spotted when using on FMRIB servers ). This simplest fix is to "call" commands.txt via sh, this change should be effectively transparent for cluster submission.

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