gridss: add java heapSize arguments.

7 files changed, 17 insertions, 7 deletions

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} \
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} \
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 48f7cb2..d55db23 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -5,6 +5,7 @@
 , faidxAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "31g"
 }:
 
 with nixpkgs;
@@ -31,7 +32,7 @@ stdenv.mkDerivation rec {
       ln -s $f
     done
     mkdir $out
-    java -ea -Xmx31g \
+    java -ea -Xmx${heapSize} \
 	    -Dreference_fasta="ref.fa" \
 	    -Dsamjdk.create_index=true \
 	    -Dsamjdk.use_async_io_read_samtools=true \
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index b68aeb1..17e3c46 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -3,6 +3,7 @@
 , thresholdCoverage ? 10000
 , flags ? null
 , config ? null
+, heapSize ? "1G"
 }:
 
 with nixpkgs;
@@ -21,7 +22,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ jre R ];
   buildCommand = ''
     mkdir $out
-    java -Xmx1G -cp ${bionix.gridss.jar} \
+    java -Xmx${heapSize} -cp ${bionix.gridss.jar} \
 			gridss.analysis.CollectGridssMetrics \
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			I=${input}\
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index 9267809..c462461 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -5,6 +5,7 @@
 , faidxAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "1G"
 }:
 
 with nixpkgs;
@@ -29,7 +30,7 @@ stdenv.mkDerivation rec {
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
     done
-    java -Xmx1G \
+    java -Xmx${heapSize} \
       -Dsamjdk.create_index=false \
 			-cp ${bionix.gridss.jar} gridss.ComputeSamTags \
 			REFERENCE_SEQUENCE=ref.fa \
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index 23a9d85..f484ed0 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -8,6 +8,8 @@
 , softClipsToSplitReadsAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "4g"
+
 }:
 
 with nixpkgs;
@@ -63,7 +65,7 @@ stdenv.mkDerivation rec {
     ${linkSV assembly}
     ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs}
     ${linkInput collectMetrics collectMetricsAttrs assembly}
-	  java -Xmx4g -Dsamjdk.create_index=true \
+	  java -Xmx${heapSize} -Dsamjdk.create_index=true \
       -cp ${jar} gridss.IdentifyVariants \
       REFERENCE_SEQUENCE=ref.fa \
       ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 9bce063..68ea0a5 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -5,6 +5,8 @@
 , alignerStreaming ? false
 , flags ? null
 , config ? null
+, heapSize ? "2G"
+
 }:
 
 with nixpkgs;
@@ -26,7 +28,7 @@ stdenv.mkDerivation rec {
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
     done
-    java -Xmx2G -Dsamjdk.create_index=false \
+    java -Xmx${heapSize} -Dsamjdk.create_index=false \
       -cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \
 			REFERENCE_SEQUENCE=ref.fa \
 			I=${input} \