From 6288d18de708695b9bae4ef37f2db672d6fb66c8 Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Mon, 24 Dec 2018 19:06:42 +0700
Subject: academic/hyphy: Updated for version 2.3.14.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/hyphy/README           |  4 ++++
 academic/hyphy/hyphy.SlackBuild | 21 ++++++++++++---------
 academic/hyphy/hyphy.info       |  8 ++++----
 3 files changed, 20 insertions(+), 13 deletions(-)

(limited to 'academic/hyphy')

diff --git a/academic/hyphy/README b/academic/hyphy/README
index 720613c4e4..4405702da1 100644
--- a/academic/hyphy/README
+++ b/academic/hyphy/README
@@ -47,6 +47,10 @@ Registration
 you are highly advised to fill the registration form found at:
 https://veg.github.io/hyphy-site/register/
 
+NOTE!
+The script builds two executables: HYPHYMP, which uses pthreads to do
+multiprocessing and HYPHYMPI, which uses openmpi (hence the dependency).
+
 Citing
 Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
 HyPhy: hypothesis testing using phylogenies.
diff --git a/academic/hyphy/hyphy.SlackBuild b/academic/hyphy/hyphy.SlackBuild
index bbcde5d9a3..e22cf3435a 100644
--- a/academic/hyphy/hyphy.SlackBuild
+++ b/academic/hyphy/hyphy.SlackBuild
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=hyphy
-VERSION=${VERSION:-2.3.13}
+VERSION=${VERSION:-2.3.14}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -69,21 +69,24 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
   -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Fix the libraries path on 64 systems
+# Fix the libraries path on 64 systems and use our compiler flags
 sed -i "s:lib/hyphy:lib${LIBDIRSUFFIX}/hyphy:g" CMakeLists.txt
+sed -i "s:-msse3:$SLKCFLAGS:g" CMakeLists.txt
+sed -i "s:-march=corei7-avx -mtune=corei7-avx:$SLKCFLAGS:g" CMakeLists.txt
+sed -i "s:-mno-avx:$SLKCFLAGS:g" CMakeLists.txt
+sed -i "s:-mno-sse3:$SLKCFLAGS:g" CMakeLists.txt
+sed -i "s:-fsigned-char -O3:$SLKCFLAGS:g" CMakeLists.txt
 
 mkdir -p build
 cd build
   cmake \
-    -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
-    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
-    -DCMAKE_REQUIRED_FLAGS="$SLKCFLAGS" \
-    -DDEFAULT_COMPILE_FLAGS="$SLKCFLAGS" \
-    -DINSTALL_PREFIX=/usr \
+    -DCMAKE_INSTALL_PREFIX=/usr \
     -DCMAKE_BUILD_TYPE=Release ..
 
-# This builds build a HyPhy executable (HYPHYMP) using pthreads to do multiprocessing
-  make MP
+# It is actually not necessary anymore to specify here MP and HYPHYMPI,
+# as 'make' alone will attempt to build them both. However, let's leave
+# them, just in case.
+  make MP HYPHYMPI
   make install DESTDIR=$PKG
 cd ..
 
diff --git a/academic/hyphy/hyphy.info b/academic/hyphy/hyphy.info
index befc1be289..33786b6d6c 100644
--- a/academic/hyphy/hyphy.info
+++ b/academic/hyphy/hyphy.info
@@ -1,10 +1,10 @@
 PRGNAM="hyphy"
-VERSION="2.3.13"
+VERSION="2.3.14"
 HOMEPAGE="https://veg.github.io/hyphy-site/"
-DOWNLOAD="https://github.com/veg/hyphy/archive/2.3.13/hyphy-2.3.13.tar.gz"
-MD5SUM="5b78195fdd4fb42cca4edd52e178ac32"
+DOWNLOAD="https://github.com/veg/hyphy/archive/2.3.14/hyphy-2.3.14.tar.gz"
+MD5SUM="d82809929d213e236078ed4853ea3962"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES=""
+REQUIRES="openmpi"
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"
-- 
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