From 25e9aae54ef8ae2b88a7ae677b4fd20d567e1a91 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Thu, 6 Dec 2018 14:30:08 +1100
Subject: gridss: remove redundant collectGridssMetrics

---
 tools/gridss-collectGridssMetrics.nix | 34 ----------------------------------
 1 file changed, 34 deletions(-)
 delete mode 100644 tools/gridss-collectGridssMetrics.nix

diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
deleted file mode 100644
index 91e04c7..0000000
--- a/tools/gridss-collectGridssMetrics.nix
+++ /dev/null
@@ -1,34 +0,0 @@
-{ bionix
-, nixpkgs
-, thresholdCoverage ? 10000
-, flags ? null
-, config ? null
-}:
-
-with nixpkgs;
-with lib;
-with bionix.types;
-
-input:
-
-let
-  ref = matchFiletype "gridss-collectGridssMetrics" { bam = x: x.ref; } input;
-  sorted = matchFileSorting "gridss-collectGridssMetrics" { name = _: true; } input;
-in
-
-
-stdenv.mkDerivation rec {
-  name = "gridss-collectGridssMetrics";
-  buildInputs = [ jre ];
-  buildCommand = ''
-    mkdir $out
-    ln -s ${input} input.bam
-    java -Xmx1G -cp ${bionix.gridss.jar} \
-			gridss.analysis.CollectGridssMetrics \
-			${optionalString sorted "ASSUME_SORTED=true"} \
-      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
-			I=input.bam \
-			O=$out \
-			THRESHOLD_COVERAGE=${toString thresholdCoverage}
-    '';
-}
-- 
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