diff options
| author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-10 16:42:16 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-10 16:42:16 +1100 |
| commit | 6742864b8f92f5d7d56da4901486b7e83a271e23 (patch) | |
| tree | ad9d65650db23fca88b133bb70814f20e4be1cfe /tools/gridss-annotateVariants.nix | |
| parent | 238c059743605853472d172f430227e06e20b891 (diff) | |
gridss: add java heapSize arguments.
Diffstat (limited to 'tools/gridss-annotateVariants.nix')
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 4 |
1 files changed, 3 insertions, 1 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} \ |