From c3af7841394bbba1433a4e7e3e4aa225c697c81d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 10 Aug 2020 09:38:03 +1000
Subject: bwa2: update to release

---
 tools/bwa-index2.nix   |  4 +++-
 tools/bwa-mem2-app.nix | 33 ++++++++++++++++++---------------
 2 files changed, 21 insertions(+), 16 deletions(-)

(limited to 'tools')

diff --git a/tools/bwa-index2.nix b/tools/bwa-index2.nix
index f5cc69b..b02d007 100644
--- a/tools/bwa-index2.nix
+++ b/tools/bwa-index2.nix
@@ -1,5 +1,6 @@
 { bionix
 , flags ? null
+, altRegex ? "^>.*_alt$"
 }:
 
 ref:
@@ -18,6 +19,7 @@ stage {
     bwa-mem2 index ${optionalString (flags != null) flags} ref.fa
     mkdir $out
     mv ref.fa.* $out
-    grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true
+    grep -P '${altRegex}' ref.fa | tr -d '^>' > $out/idxbase.alt || true
   '';
+  stripStorePaths = false;
 }
diff --git a/tools/bwa-mem2-app.nix b/tools/bwa-mem2-app.nix
index 8cca5a5..b303485 100644
--- a/tools/bwa-mem2-app.nix
+++ b/tools/bwa-mem2-app.nix
@@ -1,15 +1,18 @@
-{ bwa, fetchFromGitHub }:
-  bwa.overrideAttrs (_:
-    {
-      name = "bwa-mem2";
-      src = fetchFromGitHub {
-        owner = "bwa-mem2";
-        repo = "bwa-mem2";
-        rev = "f882015f7f46845f72c10094a621264f78d206d8";
-        sha256 = "1wfx8j9mwbb29jw4zxp28lajmj774jy1l5x229nf065cqr2dgyqg";
-        };
-      installPhase = ''
-        mkdir -p $out/bin
-        cp bwa-mem2 $out/bin
-        '';
-      })
+{ clangStdenv, fetchFromGitHub, zlib }:
+  clangStdenv.mkDerivation rec {
+  pname = "bwa-mem2";
+  version = "2.0";
+  src = fetchFromGitHub {
+    fetchSubmodules = true;
+    owner = "bwa-mem2";
+    repo = "bwa-mem2";
+    rev = "v${version}";
+    sha256 = "0q5wqal0nfxd3yfbmxahyaiqqmsrrplnwhplcjvz1xzw7bxwwnnj";
+  };
+  buildInputs = [ zlib ];
+  installPhase = ''
+    mkdir -p $out/bin
+    cp bwa-mem2 $out/bin
+  '';
+  disableHardening = [ "pie" ];
+}
-- 
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