From 233b915bd2bfe8abe302874f7b7467ad39048a2c Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Nov 2020 07:44:19 +1100
Subject: rewrite cluster example to usse overlay

---
 examples/ex-tnpair/cluster.nix | 49 +++++++++++++++++++++++-------------------
 1 file changed, 27 insertions(+), 22 deletions(-)

(limited to 'examples')

diff --git a/examples/ex-tnpair/cluster.nix b/examples/ex-tnpair/cluster.nix
index d7537b2..8d54995 100644
--- a/examples/ex-tnpair/cluster.nix
+++ b/examples/ex-tnpair/cluster.nix
@@ -1,25 +1,30 @@
-{ bionix ? import <bionix> { }, tmpDir ? null }:
+{ tmpDir ? null }:
 
 let
-  bionix' = (bionix."${if tmpDir == null then "slurm" else "qsub"}" {
-    ppn = 24;
-    mem = 7;
-    walltime = "3:00:00";
-  } // bionix.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; }).extend
-    (self: super:
-      with self; {
-        minimap2.align = def super.minimap2.align {
-          mem = 15;
-          walltime = "16:00:00";
-        };
-        samtools = super.samtools // (with super.samtools; {
-          markdup = def markdup { walltime = "12:00:00"; };
-          fixmate = def fixmate { walltime = "10:00:00"; };
-          sort = def sort {
-            mem = 27;
-            flags = "-m 1G";
-          };
-        });
-      });
+  bionix = import <bionix> {
+    overlays = [
+      (_: super:
+        super."${if tmpDir == null then "slurm" else "qsub"}" {
+          ppn = 24;
+          mem = 7;
+          walltime = "3:00:00";
+        } // super.lib.optionalAttrs (tmpDir != null) { inherit tmpDir; })
 
-in import ./. { bionix = bionix'; }
+      (self: super:
+        with super; {
+          minimap2.align = def minimap2.align {
+            mem = 15;
+            walltime = "16:00:00";
+          };
+          samtools = with samtools; {
+            markdup = def markdup { walltime = "12:00:00"; };
+            fixmate = def fixmate { walltime = "10:00:00"; };
+            sort = def sort {
+              mem = 27;
+              flags = "-m 1G";
+            };
+          };
+        })
+    ];
+  };
+in import ./. { inherit bionix; }
-- 
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