aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--tools/gridss-annotateVariants.nix4
-rw-r--r--tools/gridss-assemble.nix3
-rw-r--r--tools/gridss-callVariants.nix3
-rw-r--r--tools/gridss-collectMetrics.nix3
-rw-r--r--tools/gridss-computeSamTags.nix3
-rw-r--r--tools/gridss-identifyVariants.nix4
-rw-r--r--tools/gridss-softClipsToSplitReads.nix4
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} \