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

@@ -10,8 +10,10 @@
 # output as the final line of output. Thne script returns
 # an exit code of non-0 if something goes wrong.
 #
-# The eddy_cpu executable is executed twice - once with
-# --nthr=1, and again with --nthr=8.
+# If called from pyfeeds, the eddy_cpu executable is
+# executed twice - once with --nthr=1, and again with
+# --nthr=6. If not called from pyfeeds, the eddy_cpu
+# executable is executed only once, with --nthr=6.
 #
 # Outputs of each eddy_<variant> executable is saved with
 # prefix ${outdir}/eddyOutput_<variant>. For example, the
@@ -52,7 +54,12 @@ done
 # the FMRIB cluster
 cpu_exes=""
 if [ -x "${exedir}/eddy_cpu" ]; then
-  cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_1"
+
+  # Only run single-threaded when running
+  # through pyfeeds
+  if [ "$PYFEEDS_TESTING" = "1" ]; then
+    cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_1"
+  fi
   cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_6"
 fi