From 81b5475f8e6045d22298df191786c54bdbbbde13 Mon Sep 17 00:00:00 2001
From: darmac <xiaojun2@hisilicon.com>
Date: Mon, 27 Apr 2020 22:55:35 +0800
Subject: Add new package: smartdenovo (#16310)

---
 .../builtin/packages/smartdenovo/aarch64.patch     | 29 +++++++++++++++++++++
 .../repos/builtin/packages/smartdenovo/package.py  | 30 ++++++++++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
 create mode 100644 var/spack/repos/builtin/packages/smartdenovo/package.py

diff --git a/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch b/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
new file mode 100644
index 0000000000..998c9b2cdf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/smartdenovo/aarch64.patch
@@ -0,0 +1,29 @@
+diff --git a/Makefile b/Makefile
+index 0802f65..3816b6e 100644
+--- a/Makefile
++++ b/Makefile
+@@ -2,9 +2,9 @@ VERSION=1.0.0
+ MINOR_VER=20140314
+ CC=gcc
+ ifdef DEBUG
+-CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
++CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ else
+-CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3
++CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ endif
+ INSTALLDIR=/usr/local/bin
+ GLIBS=-lm -lpthread
+diff --git a/ksw.c b/ksw.c
+index 15dd0f2..22641ed 100644
+--- a/ksw.c
++++ b/ksw.c
+@@ -25,7 +25,7 @@
+ 
+ #include <stdlib.h>
+ #include <stdint.h>
+-#include <emmintrin.h>
++#include "SSE2NEON.h"
+ #include "ksw.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS
diff --git a/var/spack/repos/builtin/packages/smartdenovo/package.py b/var/spack/repos/builtin/packages/smartdenovo/package.py
new file mode 100644
index 0000000000..f18b8583d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/smartdenovo/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Smartdenovo(MakefilePackage):
+    """SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore
+    (ONT) data."""
+
+    homepage = "https://github.com/ruanjue/smartdenovo"
+    git      = "https://github.com/ruanjue/smartdenovo.git"
+
+    version('master', branch='master')
+
+    depends_on('sse2neon', when='target=aarch64:')
+
+    patch('aarch64.patch', when='target=aarch64:',
+        sha256='7dd4bca28aafb0680cc1823aa58ac9000819993538e92628554666c4b3acc470')
+
+    def install(self, spec, prefix):
+        install_files = [
+            'pairaln', 'wtpre', 'wtcyc', 'wtmer', 'wtzmo', 'wtobt',
+            'wtclp', 'wtext', 'wtgbo', 'wtlay', 'wtcns', 'wtmsa'
+        ]
+        mkdirp(prefix.bin)
+        for f in install_files:
+            install(f, prefix.bin)
-- 
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