Update runEddy script to work with new multi-threaded version.

The eddy_cpu command is called twice - once with --nthr=1, and again with --nthr=8

Note that these changes will not work with the openmp eddy build, so do not merge / use this MR until threddy has been released.

eddy/runEddy

@@ -30,7 +30,7 @@ set -e
 # added by this script.
 exedir="$1"; shift;
 outdir="$1"; shift;
-eddy_args="$@"
+eddy_args=("$@")
 
 # Find all eddy_cuda* executables
 cuda_exes=""
@@ -71,15 +71,13 @@ do
   if [[ "${exe_name}" == *"cuda"* ]]; then
     fsl_sub="fsl_sub -l ${outdir} --coprocessor=cuda"
     exe="${exe_name}"
-    extra_args=""
-
   else
     # unpack eddy_cpu_nthr_N
     # into eddy_cpu --nthr=N
     fsl_sub="fsl_sub -l ${outdir} -q long.q"
     exe="${exe_name%_nthr*}"
     nthr="${exe_name#eddy_cpu_nthr_}"
-    extra_args="--nthr=${nthr}"
+    eddy_args+=("--nthr=${nthr}")
     if [ "${nthr}" != "1" ]; then
       fsl_sub="${fsl_sub} -s openmp,${nthr}"
     fi
@@ -89,7 +87,7 @@ do
   # output a job id) if we try to run a
   # cuda exe on a non-cuda-capable machine
   # or queue. So we allow it to fail.
-  jid=$(${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${extra_args} ${eddy_args} || true)
+  jid=$(${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args} || true)
   if [ "${jid}" == "" ]; then
     echo "Error submitting ${exe_name} - skipping"
     continue