diff options
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 720613c4e487..4405702da107 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 bbcde5d9a335..e22cf3435a1e 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 befc1be28952..33786b6d6c38 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" |