sci-biology/amos: Use python-single-r1 instead of python-r1

* Make build system parallel buildable
* Make build system honour AR properly

Package-Manager: Portage-2.3.3, Repoman-2.3.1

diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild
new file mode 100644 (file)
index 0000000..aa59d60
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r3.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools flag-o-matic python-single-r1
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
+       https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt4"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+       ${PYTHON_DEPS}
+       dev-perl/DBI
+       dev-perl/Statistics-Descriptive
+       sci-biology/mummer"
+
+PATCHES=(
+       "${FILESDIR}"/${P}-gcc-4.7.patch
+       "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+       "${WORKDIR}"/${P}-fix-c++14.patch
+       "${FILESDIR}"/${P}-qa-Wformat.patch
+       "${FILESDIR}"/${P}-fix-build-system.patch
+)
+
+src_prepare() {
+       default
+       eautoreconf
+
+       # prevent GCC 6 log pollution due
+       # to hash_map deprecation in C++11
+       append-cxxflags -Wno-cpp
+}
+
+src_install() {
+       default
+       python_fix_shebang "${ED%/}"/usr/bin/goBambus2
+}

diff --git a/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
new file mode 100644 (file)
index 0000000..9c824dd
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-fix-build-system.patch
@@ -0,0 +1,116 @@
+* Use proper AR and not just 'ar'
+* Fix build system to build in parallel
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -34,6 +34,7 @@
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_RANLIB
++AM_PROG_AR
+ AC_PROG_CPP
+ AC_PATH_PROG(PERL, [perl], [:])
+ AC_PATH_PROG(PYTHON, [python], [:])
+--- a/src/Align/Makefile.am
++++ b/src/Align/Makefile.am
+@@ -133,7 +133,7 @@
+ 
+ ##-- hash-overlap
+ hash_overlap_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -172,7 +172,7 @@
+ 
+ ##-- make-consensus
+ make_consensus_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -182,7 +182,7 @@
+ 
+ ##-- make-consensus_poly
+ make_consensus_poly_LDADD = \
+-      $(top_builddir)/src/Align/libAlign_poly.a \
++      libAlign_poly.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -192,7 +192,7 @@
+ 
+ ##-- maligntest
+ maligntest_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -202,7 +202,7 @@
+ 
+ ##-- merge-contigs
+ merge_contigs_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -235,7 +235,7 @@
+ 
+ ##-- show-ma-asm
+ show_ma_asm_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/Common/libCommon.a \
+       $(top_builddir)/src/AMOS/libAMOS.a
+ show_ma_asm_SOURCES = \
+@@ -261,7 +261,7 @@
+ 
+ ##-- simple-overlap
+ simple_overlap_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+@@ -272,7 +272,7 @@
+ 
+ ##-- test-align
+ test_align_LDADD = \
+-      $(top_builddir)/src/Align/libAlign.a \
++      libAlign.a \
+       $(top_builddir)/src/CelMsg/libCelMsg.a \
+       $(top_builddir)/src/Slice/libSlice.a \
+       $(top_builddir)/src/Common/libCommon.a \
+--- a/src/Bambus/Bundler/Makefile.am
++++ b/src/Bambus/Bundler/Makefile.am
+@@ -47,7 +47,7 @@
+       clk.cc
+ 
+ MarkRepeats_LDADD = \
+-      $(top_builddir)/src/Bambus/Bundler/libBundler.a \
++      libBundler.a \
+       $(top_builddir)/src/Common/libCommon.a \
+       $(top_builddir)/src/AMOS/libAMOS.a \
+       $(top_builddir)/src/GNU/libGNU.a
+@@ -55,7 +55,7 @@
+       MarkRepeats.cc
+ 
+ OrientContigs_LDADD = \
+-      $(top_builddir)/src/Bambus/Bundler/libBundler.a \
++      libBundler.a \
+       $(top_builddir)/src/Common/libCommon.a \
+       $(top_builddir)/src/AMOS/libAMOS.a \
+       $(top_builddir)/src/GNU/libGNU.a
+@@ -63,7 +63,7 @@
+       OrientContigs.cc
+ 
+ FilterEdgesByCluster_LDADD = \
+-      $(top_builddir)/src/Bambus/Bundler/libBundler.a \
++      libBundler.a \
+       $(top_builddir)/src/Common/libCommon.a \
+       $(top_builddir)/src/AMOS/libAMOS.a \
+       $(top_builddir)/src/GNU/libGNU.a