From a621b614ba777c406403d18693368836a25a55f1 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 28 Sep 2018 10:26:38 +1000
Subject: Add crumble

---
 default.nix              |  1 +
 tools/crumble-app.nix    | 15 +++++++++++++++
 tools/crumble-toCram.nix | 15 +++++++++++++++
 tools/crumble.nix        |  7 +++++++
 4 files changed, 38 insertions(+)
 create mode 100644 tools/crumble-app.nix
 create mode 100644 tools/crumble-toCram.nix
 create mode 100644 tools/crumble.nix

diff --git a/default.nix b/default.nix
index 25bbf34..7ba7a1e 100644
--- a/default.nix
+++ b/default.nix
@@ -5,6 +5,7 @@ let
     let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; };
     in with self; {
       bwa = callBionix ./tools/bwa.nix;
+      crumble = callBionix ./tools/crumble.nix;
       fastqc = callBionix ./tools/fastqc.nix;
       gridss = callBionix ./tools/gridss.nix;
       mosdepth = callBionix ./tools/mosdepth.nix;
diff --git a/tools/crumble-app.nix b/tools/crumble-app.nix
new file mode 100644
index 0000000..fc30d5a
--- /dev/null
+++ b/tools/crumble-app.nix
@@ -0,0 +1,15 @@
+{stdenv, fetchFromGitHub, autoreconfHook, htslib}:
+
+stdenv.mkDerivation rec {
+  name = "crumble-${version}";
+  version = "git";
+
+  src = fetchFromGitHub {
+    owner = "jkbonfield";
+    repo = "crumble";
+    rev = "217fa927a5fffe7dfeed9ebf25ae78d5b513afac";
+    sha256 = "1sjgbz0dj9pszxqgkrslcdx305s50a5gyx3f5ajsnm4bynsjmv9i";
+  };
+
+  buildInputs = [ autoreconfHook htslib ];
+}
diff --git a/tools/crumble-toCram.nix b/tools/crumble-toCram.nix
new file mode 100644
index 0000000..6b2431f
--- /dev/null
+++ b/tools/crumble-toCram.nix
@@ -0,0 +1,15 @@
+{ stdenv
+, lib
+, callPackage
+, crumble ? callPackage ./crumble-app.nix {}
+, flags ? null}:
+
+with lib;
+
+input:
+
+stdenv.mkDerivation {
+  name = "crumble";
+  buildInputs = [ crumble ];
+  buildCommand = "crumble ${optionalString (flags != null) flags} ${input} $out";
+}
diff --git a/tools/crumble.nix b/tools/crumble.nix
new file mode 100644
index 0000000..4798329
--- /dev/null
+++ b/tools/crumble.nix
@@ -0,0 +1,7 @@
+{ bionix, nixpkgs }:
+
+with nixpkgs;
+
+{
+  toCram = attrs: callPackage ./crumble-toCram.nix attrs;
+}
-- 
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