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| author | Petar Petrov <slackalaxy@gmail.com> | 2018-12-24 19:06:42 +0700 |
|---|---|---|
| committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2018-12-24 22:16:52 +0700 |
| commit | 6288d18de708695b9bae4ef37f2db672d6fb66c8 (patch) | |
| tree | 1a383ce56504242acaa232c86888911d55cda798 /academic | |
| parent | 2183ac8328445578506cf475014eb1bf51353504 (diff) | |
| download | slackbuilds-6288d18de708695b9bae4ef37f2db672d6fb66c8.tar.gz | |
academic/hyphy: Updated for version 2.3.14.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/hyphy/README | 4 | ||||
| -rw-r--r-- | academic/hyphy/hyphy.SlackBuild | 21 | ||||
| -rw-r--r-- | academic/hyphy/hyphy.info | 8 |
3 files changed, 20 insertions, 13 deletions
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" |