[gentoo-commits] proj/sci:master commit in: sci-biology/amos/

[Martin Mokrejs]

commit:     8a1a5bf1ebdff1e93246e54e4d922bd2d5fdd18e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 23 21:25:13 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 23 21:25:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a1a5bf1

sci-biology/amos: add qt3support requirement so that we actually compile 
hawkeye, add mpi to IUSE, drop mis-placed *.pm files, cleanup deps

Package-Manager: portage-2.2.18

 sci-biology/amos/amos-3.1.0-r2.ebuild | 24 ++++++++----------------
 sci-biology/amos/amos-9999.ebuild     |  5 ++++-
 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 eadcc43..fd81df6 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 110e7c7..c47a5b6 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
 }