diff options
Diffstat (limited to 'tools/gridss-collectMetrics.nix')
-rw-r--r-- | tools/gridss-collectMetrics.nix | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix new file mode 100644 index 0000000..4688808 --- /dev/null +++ b/tools/gridss-collectMetrics.nix @@ -0,0 +1,30 @@ +{ bionix +, nixpkgs +, thresholdCoverage ? 10000 +, flags ? null +}: + +with nixpkgs; +with lib; +with bionix.types; + +input: + +let + ref = matchFiletype "gridss-collectMetrics" { bam = x: x.ref; } input; +in + + +stdenv.mkDerivation rec { + name = "gridss-collectMetrics"; + buildInputs = [ jre R ]; + buildCommand = '' + mkdir $out + java -Xmx1G -cp ${bionix.gridss.jar} \ + gridss.analysis.CollectGridssMetrics \ + I=${input}\ + O=$out/input \ + AS=true \ + THRESHOLD_COVERAGE=${toString thresholdCoverage} + ''; +} |