diff options
Diffstat (limited to 'tools/gridss-assemble.nix')
| -rw-r--r-- | tools/gridss-assemble.nix | 4 |
1 files changed, 3 insertions, 1 deletions
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} \ |