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-rw-r--r--sci-biology/augustus/ChangeLog9
-rw-r--r--sci-biology/augustus/augustus-2.3.1.ebuild6
-rw-r--r--sci-biology/augustus/augustus-2.4.ebuild4
-rw-r--r--sci-biology/augustus/augustus-2.5.5.ebuild50
-rw-r--r--sci-biology/augustus/augustus-2.5.ebuild4
-rw-r--r--sci-biology/augustus/files/augustus-2.5.5-sane-build.patch156
6 files changed, 221 insertions, 8 deletions
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
index 0b75a6b86202..6be9176fcc61 100644
--- a/sci-biology/augustus/ChangeLog
+++ b/sci-biology/augustus/ChangeLog
@@ -1,6 +1,13 @@
# ChangeLog for sci-biology/augustus
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.14 2011/03/09 22:54:02 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.15 2011/06/23 14:58:14 jlec Exp $
+
+*augustus-2.5.5 (23 Jun 2011)
+
+ 23 Jun 2011; Justin Lecher <jlec@gentoo.org> augustus-2.3.1.ebuild,
+ augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild,
+ +files/augustus-2.5.5-sane-build.patch:
+ Version Bump, respect LDFLAGS, #337655
09 Mar 2011; Markos Chandras <hwoarang@gentoo.org> augustus-2.4.ebuild:
Stable on amd64 wrt bug #353573
diff --git a/sci-biology/augustus/augustus-2.3.1.ebuild b/sci-biology/augustus/augustus-2.3.1.ebuild
index cbcfebcf8c5f..9790356ed4a8 100644
--- a/sci-biology/augustus/augustus-2.3.1.ebuild
+++ b/sci-biology/augustus/augustus-2.3.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.3.1.ebuild,v 1.3 2010/02/09 11:13:18 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.3.1.ebuild,v 1.4 2011/06/23 14:58:14 jlec Exp $
-EAPI="2"
+EAPI=2
inherit base eutils
diff --git a/sci-biology/augustus/augustus-2.4.ebuild b/sci-biology/augustus/augustus-2.4.ebuild
index a2a83835f179..b12297409483 100644
--- a/sci-biology/augustus/augustus-2.4.ebuild
+++ b/sci-biology/augustus/augustus-2.4.ebuild
@@ -1,8 +1,8 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.4.ebuild,v 1.6 2011/03/09 22:54:02 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.4.ebuild,v 1.7 2011/06/23 14:58:14 jlec Exp $
-EAPI="2"
+EAPI=2
inherit base eutils
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild
new file mode 100644
index 000000000000..3bbf25951425
--- /dev/null
+++ b/sci-biology/augustus/augustus-2.5.5.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.5.ebuild,v 1.1 2011/06/23 14:58:14 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://augustus.gobics.de/"
+SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+
+S="${WORKDIR}/${PN}.${PV}"
+
+src_prepare() {
+ epatch "${FILESDIR}"/${P}-sane-build.patch
+ tc-export CC CXX
+}
+
+src_compile() {
+ emake clean && emake
+}
+
+src_install() {
+ dobin bin/*
+# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
+
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*.p*
+ insinto /usr/libexec/${PN}
+ doins scripts/*.conf
+
+ insinto /usr/share/${PN}
+ doins -r config
+
+ echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+
+ dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
+
+ if use examples; then
+ insinto /usr/share/${PN}/
+ doins -r docs/tutorial examples
+ fi
+}
diff --git a/sci-biology/augustus/augustus-2.5.ebuild b/sci-biology/augustus/augustus-2.5.ebuild
index 4fad0c1f0605..33db1bfc1c8c 100644
--- a/sci-biology/augustus/augustus-2.5.ebuild
+++ b/sci-biology/augustus/augustus-2.5.ebuild
@@ -1,8 +1,8 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.ebuild,v 1.4 2011/02/07 08:06:05 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.ebuild,v 1.5 2011/06/23 14:58:14 jlec Exp $
-EAPI="2"
+EAPI=2
inherit base eutils
diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
new file mode 100644
index 000000000000..39cd0762b1c1
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch
@@ -0,0 +1,156 @@
+ Makefile | 8 +++---
+ scripts/Makefile | 6 +++-
+ scripts/aln2wig/Makefile | 8 +++---
+ scripts/compileSpliceCands/Makefile | 6 ++--
+ src/Makefile | 43 ++++++++++++++++++----------------
+ 5 files changed, 38 insertions(+), 33 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e23a667..64610c8 100644
+--- a/Makefile
++++ b/Makefile
+@@ -3,9 +3,9 @@
+ #
+
+ all:
+- cd src && ${MAKE}
+- cd scripts && ${MAKE}
++ $(MAKE) -C src
++ $(MAKE) -C scripts
+
+ clean:
+- cd src && ${MAKE} clean
+- cd scripts && ${MAKE} clean
++ $(MAKE) -C src clean
++ $(MAKE) -C scripts clean
+diff --git a/scripts/Makefile b/scripts/Makefile
+index 6d4dd67..ab6a885 100644
+--- a/scripts/Makefile
++++ b/scripts/Makefile
+@@ -1,5 +1,7 @@
+ all :
+- cd aln2wig && ${MAKE}
++ $(MAKE) -C aln2wig
++ $(MAKE) -C compileSpliceCands
+
+ clean :
+- cd aln2wig && ${MAKE} clean
++ $(MAKE) -C aln2wig clean
++ $(MAKE) -C compileSpliceCands
+diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile
+index 64d09f5..9752980 100644
+--- a/scripts/aln2wig/Makefile
++++ b/scripts/aln2wig/Makefile
+@@ -1,10 +1,10 @@
+-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb
++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic
+
+ psl2wig : aln2wig.o
+- gcc $(CFLAGS) -o aln2wig aln2wig.o;
+- cp aln2wig ../../bin
++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
++ cp aln2wig ../../bin/
+ psl2wig.o : aln2wig.c
+- gcc $(CFLAGS) -c aln2wig.c
++ $(CC) $(CFLAGS) -c aln2wig.c
+
+ all : psl2wig
+
+diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile
+index cddada5..8079791 100644
+--- a/scripts/compileSpliceCands/Makefile
++++ b/scripts/compileSpliceCands/Makefile
+@@ -1,8 +1,8 @@
+ compileSpliceCands : compileSpliceCands.o list.h list.o
+- gcc -o compileSpliceCands compileSpliceCands.o list.o;
+-# cp compileSpliceCands ../../bin
++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
++ cp compileSpliceCands ../../bin/
+ compileSpliceCands.o : compileSpliceCands.c
+- gcc -Wall -pedantic -ansi -c compileSpliceCands.c
++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c
+
+ all : compileSpliceCands
+
+diff --git a/src/Makefile b/src/Makefile
+index 71795b6..732b953 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,8 +6,8 @@
+ # a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
+ # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
+ #
+-CC = g++
+-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static
++CXX ?= g++
++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static
+ INCLS = -I../include -I.
+ LIBS = # -lcwd
+ OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \
+@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte
+ PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign
+ INFO = cflags
+
+-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info
++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin
+
+ .SUFFIXES:
+ .SUFFIXES: .cc .o .so
+
+ .cc.o:
+- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS)
++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS)
+
+-augustus: augustus.cc $(OBJS) $(DUMOBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++bin: $(PROGR)
++ cp $(PROGR) ../bin/
++
++augustus: augustus.o $(OBJS) $(DUMOBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp augustus ../bin/
+
+-etraining: etraining.cc $(TOBJS) $(OBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++etraining: etraining.o $(TOBJS) $(OBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp etraining ../bin/
+
+-evaluate: evaluate.cc $(OBJS) $(DUMOBJS)
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++evaluate: evaluate.o $(OBJS) $(DUMOBJS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-consensusFinder: consensusFinder.cc consensus.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++consensusFinder: consensusFinder.o consensus.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-curve2hints: curve2hints.cc exon_seg.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++curve2hints: curve2hints.o exon_seg.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+
+-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \
++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \
+ types.o properties.o geneticcode.o pp_profile.o lldouble.o
+- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS)
+ cp fastBlockSearch ../bin/
+
+-prepareAlign: pp_prepare_align.cc
+- $(CC) $(CFLAGS) -o $@ $^
++prepareAlign: pp_prepare_align.o
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^
+ cp prepareAlign ../bin/
+
+ info:
+- echo "$(CFLAGS)" > $(INFO)
++ echo "$(CXXFLAGS)" > $(INFO)
+
+ clean:
+- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO)
++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/*
+
+ tidy: clean
+ rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)