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| author | Justin Bedo <cu@cua0.org> | 2019-02-11 09:11:36 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-02-11 09:13:00 +1100 |
| commit | bb7d6dce2f5f9ad4ebc39a80eff9e4cf66b34a28 (patch) | |
| tree | 1a80963b7a79489df8f90d92932bd46b7a8dbb73 | |
| parent | de57ab52a839ffbd5eee90aca29d6042b4911ed2 (diff) | |
snpeff: parameterise heap size and default to 31g
| -rw-r--r-- | tools/snpeff-annotate.nix | 2 | ||||
| -rw-r--r-- | tools/snpeff-dbnsfp.nix | 2 |
2 files changed, 4 insertions, 0 deletions
diff --git a/tools/snpeff-annotate.nix b/tools/snpeff-annotate.nix index dee99f1..317d303 100644 --- a/tools/snpeff-annotate.nix +++ b/tools/snpeff-annotate.nix @@ -1,5 +1,6 @@ {bionix ,db +,heapSize ? "31g" ,flags ? ""}: input: @@ -12,6 +13,7 @@ assert (matchFiletype "snpeff-annotate" { vcf = _: true; } input); stage { name = "snpeff-annotate"; buildInputs = with pkgs; [ snpeff ]; + JAVA_TOOL_OPTIONS = "-Xmx${heapSize}"; buildCommand = '' ln -s ${db} ${db.name} snpeff -nodownload -dataDir $TMPDIR ${db.name} ${input} > $out diff --git a/tools/snpeff-dbnsfp.nix b/tools/snpeff-dbnsfp.nix index 1d144cd..518c121 100644 --- a/tools/snpeff-dbnsfp.nix +++ b/tools/snpeff-dbnsfp.nix @@ -1,5 +1,6 @@ {bionix ,dbnsfp +,heapSize ? "31g" ,flags ? ""}: input: @@ -11,6 +12,7 @@ assert (matchFiletype "snpeff-dbnsfp" { vcf = _: true; } input); stage { name = "snpeff-dbnsfp"; + JAVA_TOOL_OPTIONS = "-Xmx${heapSize}"; buildCommand = '' ln -s ${dbnsfp.db} dbNSFP.txt.gz ln -s ${dbnsfp.index} dbNSFP.txt.gz.tbi |