diff options
Diffstat (limited to 'tools/gridss-variants.nix')
| -rw-r--r-- | tools/gridss-variants.nix | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index a838da6..eb5957f 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -8,6 +8,7 @@ , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } , flags ? null , config ? null +, heapSize ? "4g" }: with nixpkgs; @@ -68,7 +69,7 @@ rec { name = "gridss-identifyVariants"; buildInputs = [ jre samtools ]; buildCommand = mkLinks + '' - 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} \ @@ -91,7 +92,7 @@ rec { buildInputs = [ jre ]; buildCommand = mkLinks + '' ln -s ${identify} input.vcf - java -Xmx4g -Dsamjdk.create_index=true \ + java -Xmx${heapSize} -Dsamjdk.create_index=true \ -cp ${jar} gridss.AnnotateVariants \ REFERENCE_SEQUENCE=ref.fa \ ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \ |