proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 212 insertions, 0 deletions

diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
new file mode 100644
index 000000000000..cdfb577937e0
--- /dev/null
+++ b/sci-biology/augustus/Manifest
@@ -0,0 +1 @@
+DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a
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..e58be6db6d6a
--- /dev/null
+++ b/sci-biology/augustus/augustus-2.5.5.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/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)
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/augustus/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>