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-rw-r--r--sci-biology/amos/amos-3.1.0-r2.ebuild20
-rw-r--r--sci-biology/amos/amos-9999.ebuild21
-rw-r--r--sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch43
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()