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-annotateVariants.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index df3b1bd..d5390b9 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -9,6 +9,8 @@
 , identifyVariantsAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "4g"
+
 }:
 
 with nixpkgs;
@@ -66,7 +68,7 @@ stdenv.mkDerivation rec {
     ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs}
     ${linkInput collectMetrics collectMetricsAttrs assembly}
     ln -s ${identifyVariants identifyVariantsAttrs inputs} input.vcf
-	  java -Xmx4g -Dsamjdk.create_index=true \
+	  java -Xmx${heapSize} -Dsamjdk.create_index=true \
       -cp ${jar} gridss.AnnotateVariants \
       REFERENCE_SEQUENCE=ref.fa \
       ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
-- 
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