diff options
| -rw-r--r-- | sci-biology/amos/amos-3.1.0-r2.ebuild | 20 | ||||
| -rw-r--r-- | sci-biology/amos/amos-9999.ebuild | 21 | ||||
| -rw-r--r-- | sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch | 43 |
3 files changed, 71 insertions, 13 deletions
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild index d4107d509..951f12c1b 100644 --- a/sci-biology/amos/amos-3.1.0-r2.ebuild +++ b/sci-biology/amos/amos-3.1.0-r2.ebuild @@ -16,13 +16,12 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi qt4" +IUSE="mpi qt5" DEPEND=" mpi? ( virtual/mpi ) dev-libs/boost - qt4? ( dev-qt/qtcore:4[qt3support] - dev-qt/qt3support:4 ) + qt5? ( dev-qt/qtcore:5 ) sci-biology/blat sci-biology/jellyfish:1" RDEPEND="${DEPEND} @@ -36,13 +35,24 @@ MAKEOPTS+=" -j1" src_prepare() { epatch \ "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch \ + "${FILESDIR}"/${P}-rename_to_jellyfish1.patch # $ gap-links # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/ # $ + sh ./bootstrap || die + default + eautoreconf + # prevent GCC 6 log pollution due to hash_map deprecation in C++11 + # shutdown gcc-8.2.0 messages too + append-cxxflags -Wno-cpp -Wno-narrowing } -# --with-jellyfish location of Jellyfish headers +src_configure() { + local myconf + use X && myconf+=( --with-x ) + econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all +} src_install() { default diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild index 55eb97e1a..923ac5978 100644 --- a/sci-biology/amos/amos-9999.ebuild +++ b/sci-biology/amos/amos-9999.ebuild @@ -19,13 +19,12 @@ EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos" LICENSE="Artistic" SLOT="0" KEYWORDS="" -IUSE="mpi qt4" +IUSE="mpi qt5 X" DEPEND=" mpi? ( virtual/mpi ) dev-libs/boost - qt4? ( dev-qt/qtcore:4[qt3support] - dev-qt/qt3support:4 ) + qt5? ( dev-qt/qtcore:5 ) sci-biology/blat sci-biology/jellyfish:1" RDEPEND="${DEPEND} @@ -33,20 +32,26 @@ RDEPEND="${DEPEND} dev-perl/Statistics-Descriptive sci-biology/mummer" -# --with-jellyfish location of Jellyfish headers - # $ gap-links # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/ # $ src_prepare() { epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch + epatch "${FILESDIR}"/amos-3.1.0-rename_to_jellyfish1.patch + sh ./bootstrap || die default eautoreconf - # prevent GCC 6 log pollution due - # to hash_map deprecation in C++11 - append-cxxflags -Wno-cpp + # prevent GCC 6 log pollution due to hash_map deprecation in C++11 + # shutdown gcc-8.2.0 messages too + append-cxxflags -Wno-cpp -Wno-narrowing +} + +src_configure() { + local myconf + use X && myconf+=( --with-x ) + econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all } src_install() { diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch new file mode 100644 index 000000000..4b52c5640 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch @@ -0,0 +1,43 @@ +--- config/amos.m4 2018-09-11 13:23:14.478444129 +0200 ++++ config/amos.m4 2018-09-11 13:36:36.697612245 +0200 +@@ -695,15 +695,15 @@ + else + jellyfish_unspecified=no + fi +-if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then ++if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then + if test $jellyfish_unspecified = no; then +- AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"]) ++ AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"]) + fi + JELLYFISH_LDADD= + JELLYFISH_CPPFLAGS= + AC_MSG_RESULT([not found]) + else +- JELLYFISH_LDADD="-ljellyfish -lpthread" ++ JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread" + JELLYFISH_CPPFLAGS="-I $jellyfish_dir" + AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish]) + cppflags_save="$CPPFLAGS" +@@ -715,7 +715,7 @@ + AC_LANG_PUSH([C++]) + AC_LINK_IFELSE([ + AC_LANG_PROGRAM([ +-#include <jellyfish/mer_counting.hpp> ++#include <jellyfish1/mer_counting.hpp> + #include <string> + ], [ + std::string s; +--- src/Align/kmer-cov-plot.cc 2018-09-11 13:23:15.079443556 +0200 ++++ src/Align/kmer-cov-plot.cc 2018-09-11 13:36:36.831612096 +0200 +@@ -388,8 +388,8 @@ + + #ifdef WITH_JELLYFISH + +-#include <jellyfish/compacted_hash.hpp> +-#include <jellyfish/mer_counting.hpp> ++#include <jellyfish1/compacted_hash.hpp> ++#include <jellyfish1/mer_counting.hpp> + + // Assert that jellyfish is using the expected kmer representation + static void jellyfish_check() |