From cdb7056a14915354d879c519dd396204e4af3959 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 10 Apr 2020 09:47:44 +1000
Subject: update tnpair example to run on colo828

---
 examples/ex-tnpair/cluster.nix | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 examples/ex-tnpair/cluster.nix

(limited to 'examples/ex-tnpair/cluster.nix')

diff --git a/examples/ex-tnpair/cluster.nix b/examples/ex-tnpair/cluster.nix
new file mode 100644
index 0000000..d7537b2
--- /dev/null
+++ b/examples/ex-tnpair/cluster.nix
@@ -0,0 +1,25 @@
+{ bionix ? import <bionix> { }, 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";
+          };
+        });
+      });
+
+in import ./. { bionix = bionix'; }
-- 
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