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-rw-r--r--var/spack/repos/builtin/packages/smartdenovo/aarch64.patch29
-rw-r--r--var/spack/repos/builtin/packages/smartdenovo/package.py30
2 files changed, 59 insertions, 0 deletions
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)