From 5e2c7c85d001fde0600e77bfbd9d1078fcd561f4 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Feb 2019 10:18:20 +1100
Subject: qsub: parameterise queue and allow arbitrary flags to be passed

---
 default.nix  |  2 +-
 lib/qsub.nix | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/default.nix b/default.nix
index f3a582b..bd68277 100644
--- a/default.nix
+++ b/default.nix
@@ -32,7 +32,7 @@ let
     strelka = callBionix ./tools/strelka.nix {};
 
     qsub = attrs: bionix.extend (self: super: with self; rec {
-      qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; } // attrs;
+      qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; queue = null; flags = null; } // attrs;
       qsub = attrs: (callPackage ./lib/qsub.nix {}) (qsubDefs // attrs);
       exec = f: x: y: qsub (builtins.intersectAttrs qsubDefs x) (f (builtins.removeAttrs x (builtins.attrNames qsubDefs)) y);
     });
diff --git a/lib/qsub.nix b/lib/qsub.nix
index 53e5780..85036fb 100644
--- a/lib/qsub.nix
+++ b/lib/qsub.nix
@@ -1,6 +1,8 @@
 {stdenv, lib, writeScript}:
 
-{ ppn, mem, walltime, tmpDir, sleepTime}: drv: lib.overrideDerivation drv ({ args, builder, name, ... }: {
+with lib;
+
+{ ppn, mem, walltime, queue ? null, flags ? null, tmpDir, sleepTime}: drv: lib.overrideDerivation drv ({ args, builder, name, ... }: {
   builder = "/bin/bash";
   args = let
     script = writeScript "qsub-script" ''
@@ -27,7 +29,11 @@
       NIX_BUILD_CORES=${toString ppn}
 
       while : ; do
-        qsub -l nodes=1:ppn=${toString ppn},mem=${toString mem}gb,walltime=${walltime} -N "${name}" ${script} 2>&1 > id
+        qsub -l nodes=1:ppn=${toString ppn},mem=${toString mem}gb,walltime=${walltime} \
+          -N "${name}" \
+          ${optionalString (queue != null) "-q ${queue}"} \
+          ${optionalString (flags != null) flags} \
+          ${script} 2>&1 > id
         if [ $? -eq 0 ] ; then
           break
         fi
-- 
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