Major re-arrangement of eddy tests

so that job submission / monitoring code is shared across all tests in a common runEddy script. Also test both $FSLDIR/bin/eddy_openmp and $FSLDIR/bin/eddy_cpu if either exist. Tests can be executed either on a cluster submission node, or locally

eddy/runEddy

@@ -19,7 +19,7 @@
 
 set -e
 
-# First argument is directory in which to search 
+# First argument is directory in which to search
 # for eddy executables (typically $FSLDIR/bin).
 # All remaining arguments are to be passed to
 # eddy. Don't pass the --out option, as that is
@@ -60,7 +60,7 @@ for exe in ${cuda_exes} ${cpu_exes};
 do
   variant=`basename ${exe}`
   variant=`echo ${variant} | sed 's/eddy_//'`
-  
+
   if [[ "${exe}" == *"cuda"* ]]; then
     fsl_sub="fsl_sub -l ${outdir} -q cuda.q"
   else
@@ -72,12 +72,12 @@ do
     echo "Error submitting ${exe} ${eddy_args}"
     exit 1
   fi
-  
+
   if [[ "${exe}" == *"cuda"* ]]; then
     cuda_jids="${cuda_jids} ${jid}"
   else
     cpu_jids="${cpu_jids} ${jid}"
-  fi  
+  fi
 done
 
 # If running on a cluster, wait
@@ -87,7 +87,7 @@ done
 # have blocked until completion.
 if [ ! -z "${SGE_ROOT}" ]; then
 
-  # Ensure that slots are being reserved 
+  # Ensure that slots are being reserved
   # on the queue for CPU jobs
   for jid in ${cpu_jids}; do
     qalter ${jid} -R y
@@ -111,12 +111,12 @@ if [ ! -z "${SGE_ROOT}" ]; then
 fi
 
 # Gather output prefixes for each run,
-# and check that the main output file 
+# and check that the main output file
 # was created
 outputs=""
 for exe in ${cuda_exes} ${cpu_exes};
 do
-  tmp=`basename ${cuda_exe}`
+  tmp=`basename ${exe}`
   variant=`echo ${tmp} | sed 's/eddy_//'`
   prefix="${outdir}/eddyOutput_${variant}"
   outputs="${outputs} ${prefix}"