diff options
Diffstat (limited to 'tools/gridss-annotateVariants.nix')
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 5 |
1 files changed, 4 insertions, 1 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} \ |