From 6742864b8f92f5d7d56da4901486b7e83a271e23 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Mon, 10 Dec 2018 16:42:16 +1100
Subject: gridss: add java heapSize arguments.

---
 tools/gridss-assemble.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'tools/gridss-assemble.nix')

diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index b24f742..00408d6 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -6,6 +6,7 @@
 , collectMetricsAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "31g"
 }:
 
 with nixpkgs;
@@ -46,7 +47,7 @@ stdenv.mkDerivation rec {
       ln -s $f
     done
     ${concatMapStringsSep "\n" linkInput inputs}
-	  java -Xmx31g -Dsamjdk.create_index=true \
+	  java -Xmx${heapSize} -Dsamjdk.create_index=true \
       -cp ${bionix.gridss.jar} gridss.AssembleBreakends \
       REFERENCE_SEQUENCE=ref.fa \
       ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
-- 
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