Allowing configuration of cuda parameters

bip/pipelines/dMRI_diff/__init__.py

@@ -21,17 +21,16 @@ def add_to_pipeline(ctx, pipe, tree):
 
     subj = ctx.subject
 
-    # TODO: Make this configurable
-    cuda_eddy_dict = dict(queue="short.qg@@win-uk-biobank-gpu",
-                          coprocessor="cuda",
-                          coprocessor_class="P",
-                          coprocessor_toolkit="8.0",
+    cuda_eddy_dict = dict(queue=ctx.get("queue_cuda"),
+                          coprocessor=ctx.get("sge_coprocessor"),
+                          coprocessor_class=ctx.get("sge_coprocessor_class"),
+                          coprocessor_toolkit=ctx.get("sge_cuda_toolkit_eddy"),
                           name=job_name(diff_eddy.run, subj))
 
-    cuda_bedpostx_dict = dict(queue="short.qg@@win-uk-biobank-gpu",
-                              coprocessor="cuda",
-                              coprocessor_class="P",
-                              coprocessor_toolkit="6.5",
+    cuda_bedpostx_dict = dict(queue=ctx.get("queue_cuda"),
+                              coprocessor=ctx.get("sge_coprocessor"),
+                              coprocessor_class=ctx.get("sge_coprocessor_class"),
+                              coprocessor_toolkit=ctx.get("sge_cuda_toolkit_bedpostx"),
                               name=job_name(diff_bedpostx.run, subj))
     pipe(diff_eddy.run,
          submit=cuda_eddy_dict,