8 files changed, 19 insertions, 41 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 3560f77..e0a6f0f 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -9,6 +9,8 @@
 , identifyVariantsAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "4g"
+
 }:
 
 with nixpkgs;
@@ -55,6 +57,7 @@ stdenv.mkDerivation rec {
   name = "gridss-identifyVariants";
   buildInputs = [ jre ];
   buildCommand = ''
+    TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
@@ -65,7 +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 a8124e0..f57bc12 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -6,6 +6,7 @@
 , collectMetricsAttrs ? {}
 , flags ? null
 , config ? null
+, heapSize ? "31g"
 }:
 
 with nixpkgs;
@@ -39,13 +40,14 @@ stdenv.mkDerivation rec {
   name = "gridss-assemble";
   buildInputs = [ jre bwa ];
   buildCommand = ''
+    TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       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-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
deleted file mode 100644
index 91e04c7..0000000
--- a/tools/gridss-collectGridssMetrics.nix
+++ /dev/null
@@ -1,34 +0,0 @@
-{ bionix
-, nixpkgs
-, thresholdCoverage ? 10000
-, flags ? null
-, config ? null
-}:
-
-with nixpkgs;
-with lib;
-with bionix.types;
-
-input:
-
-let
-  ref = matchFiletype "gridss-collectGridssMetrics" { bam = x: x.ref; } input;
-  sorted = matchFileSorting "gridss-collectGridssMetrics" { name = _: true; } input;
-in
-
-
-stdenv.mkDerivation rec {
-  name = "gridss-collectGridssMetrics";
-  buildInputs = [ jre ];
-  buildCommand = ''
-    mkdir $out
-    ln -s ${input} input.bam
-    java -Xmx1G -cp ${bionix.gridss.jar} \
-			gridss.analysis.CollectGridssMetrics \
-			${optionalString sorted "ASSUME_SORTED=true"} \
-      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
-			I=input.bam \
-			O=$out \
-			THRESHOLD_COVERAGE=${toString thresholdCoverage}
-    '';
-}
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 c23168f..c5d8062 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} \