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-softClipsToSplitReads.nix | |
| parent | 238c059743605853472d172f430227e06e20b891 (diff) | |
gridss: add java heapSize arguments.
Diffstat (limited to 'tools/gridss-softClipsToSplitReads.nix')
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 4 |
1 files changed, 3 insertions, 1 deletions
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} \ |