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-rw-r--r--sci-biology/amos/amos-3.1.0-r2.ebuild24
-rw-r--r--sci-biology/amos/amos-9999.ebuild5
2 files changed, 12 insertions, 17 deletions
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index eadcc4328..fd81df623 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -17,16 +17,18 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="qt4"
+IUSE="mpi qt4"
DEPEND="
+ mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4 )"
+ qt4? ( dev-qt/qtcore:4[qt3support] )
+ sci-biology/blat
+ sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-lang/perl
dev-perl/DBI
dev-perl/Statistics-Descriptive
- sci-biology/blat
sci-biology/mummer"
MAKEOPTS+=" -j1"
@@ -37,19 +39,6 @@ src_prepare() {
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
}
-# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm
-
# --with-jellyfish location of Jellyfish headers
src_install() {
@@ -64,4 +53,7 @@ src_install() {
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+ # zap the mis-placed files ('make install' is at fault)
+ rm -f "${D}"/usr/lib64/AMOS/*.pm
+ rm -rf "${D}"/usr/lib64/TIGR
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 110e7c798..c47a5b6f8 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -23,7 +23,7 @@ IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4 )
+ qt4? ( dev-qt/qtcore:4[qt3support] )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
@@ -45,4 +45,7 @@ src_install() {
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+ # zap the mis-placed files ('make install' is at fault)
+ rm -f "${D}"/usr/lib64/AMOS/*.pm
+ rm -rf "${D}"/usr/lib64/TIGR
}