From 86b1b192501eecc8a4e566795327772c32b1633d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 5 Dec 2018 10:48:05 +1100
Subject: bowtie: init

---
 tools/bowtie-index.nix | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tools/bowtie-index.nix

(limited to 'tools/bowtie-index.nix')

diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
new file mode 100644
index 0000000..98e529f
--- /dev/null
+++ b/tools/bowtie-index.nix
@@ -0,0 +1,22 @@
+{ bionix
+, nixpkgs
+, flags ? null
+, seed ? 42
+}:
+
+ref:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "bowtie-index" { fa = _: true; } ref);
+
+stdenv.mkDerivation {
+  name = "bowtie-index";
+  buildInputs = [ bowtie2 ];
+  buildCommand = ''
+    mkdir $out
+    bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
+  '';
+}
-- 
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