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

6 files changed, 241 insertions, 0 deletions

diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest
new file mode 100644
index 000000000000..fb04603869dd
--- /dev/null
+++ b/sci-biology/lagan/Manifest
@@ -0,0 +1 @@
+DIST lagan20.tar.gz 589115 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe
diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch
new file mode 100644
index 000000000000..e324ef64c4c6
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-flags.patch
@@ -0,0 +1,107 @@
+diff --git a/Makefile b/Makefile
+index fbbbe79..a1d449b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+ all:
+-	(cd src; $(MAKE))
++	$(MAKE) -C src
+ clean:
+ 	rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
+ 	(cd src; $(MAKE) clean)
+diff --git a/src/Makefile b/src/Makefile
+index 7f6b6fd..dd6309b 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
+ TRGT_DIR = ..
+ 
+ all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
+-	(cd glocal; $(MAKE))
++	$(MAKE) -C glocal
+ clean: 
+ 	rm -f *.o *~ utils/*~ mlagan.purify core
+ 	(cd glocal; $(MAKE) clean)
+ ../anchors: anchors.c skiplist.c
+-	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ ../order: order.c diagmatrix.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ ../utils/bin2mf: utils/bin2mf.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ ../utils/bin2bl: utils/bin2bl.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ ../utils/cextract: utils/cextract.c
+-	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ ../utils/cstat: utils/cstat.c
+-	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ ../utils/contigorder: utils/contigorder.c
+-	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ ../utils/getbounds: utils/getbounds.c
+-	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ ../utils/getcontigpos: utils/getcontigpos.c
+-	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ ../utils/getlength: utils/getlength.c
+-	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ ../utils/getoverlap: utils/getoverlap.c
+-	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ ../utils/rc: utils/rc.c
+-	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ ../utils/seqmerge: utils/seqmerge.c
+-	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ ../utils/scorealign: utils/scorealign.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ ../utils/scorecontigs: utils/scorecontigs.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ ../utils/fa2xfa: utils/fa2xfa.c
+-	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ ../utils/overlay: utils/overlay.c
+-	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ ../utils/Glue: utils/Glue.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ ../utils/dotplot: utils/dotplot.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+diff --git a/src/glocal/Makefile b/src/glocal/Makefile
+index ce1421a..b82507f 100755
+--- a/src/glocal/Makefile
++++ b/src/glocal/Makefile
+@@ -10,10 +10,10 @@ TRGT = glocal
+ OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
+ 
+ .cpp.o:
+-	$(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
++	$(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
+ 
+ $(TRGT): $(OBJECTS)
+-	$(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
++	$(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+ 
+ clean :
+ 	rm -f *.o ./*~ *~ core
diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
new file mode 100644
index 000000000000..a4b1d6808e2f
--- /dev/null
+++ b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
@@ -0,0 +1,23 @@
+diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
+--- lagan20-orig/src/glocal/score.cpp	2009-02-04 15:25:57.698333297 +0000
++++ lagan20/src/glocal/score.cpp	2009-02-04 15:27:23.894092890 +0000
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+ 
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+ 
+diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
+--- lagan20-orig/src/utils/Glue.cpp	2009-02-04 15:25:57.702333182 +0000
++++ lagan20/src/utils/Glue.cpp	2009-02-04 15:27:04.190822654 +0000
+@@ -1,6 +1,7 @@
+ #include "MultiSequence.h"
+ #include "SafeVector.h"
+ #include "Output.h"
++#include <string.h>
+ #include <math.h>
+ #include <assert.h>
+ #include <fstream>
diff --git a/sci-biology/lagan/lagan-2.0-r1.ebuild b/sci-biology/lagan/lagan-2.0-r1.ebuild
new file mode 100644
index 000000000000..63b966e79ef0
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils
+
+MY_P="lagan20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die
+	# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
+	sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_install() {
+	dobin lagan.pl slagan.pl mlagan
+	rm lagan.pl slagan.pl utils/Utils.pm
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins Utils.pm
+	exeinto /usr/share/${PN}/utils
+	doexe utils/*
+	exeinto /usr/share/${PN}
+	doexe *.pl anchors chaos glocal order prolagan
+	insinto /usr/share/${PN}
+	doins *.txt
+	dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap
+	dosym /usr/bin/lagan.pl /usr/bin/lagan
+	dosym /usr/bin/slagan.pl /usr/bin/slagan
+	echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN}
+	doenvd "${S}/99${PN}"
+	dodoc Readmes/README.*
+}
diff --git a/sci-biology/lagan/lagan-2.0-r2.ebuild b/sci-biology/lagan/lagan-2.0-r2.ebuild
new file mode 100644
index 000000000000..a37a3736de08
--- /dev/null
+++ b/sci-biology/lagan/lagan-2.0-r2.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="2"
+
+inherit eutils multilib toolchain-funcs
+
+MY_P="lagan20"
+
+DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA"
+HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
+SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
+	# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline
+	sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_compile() {
+	emake \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		CXXFLAGS="${CXXFLAGS}" \
+		CFLAGS="${CFLAGS}"
+}
+
+src_install() {
+	newbin lagan.pl lagan || die
+	newbin slagan.pl slagan || die
+	dobin mlagan || die
+	rm lagan.pl slagan.pl utils/Utils.pm
+
+	insinto /usr/$(get_libdir)/${PN}/lib
+	doins Utils.pm || die
+	exeinto /usr/$(get_libdir)/${PN}/utils
+	doexe utils/* || die
+	exeinto /usr/$(get_libdir)/${PN}
+	doexe *.pl anchors chaos glocal order prolagan || die
+	insinto /usr/$(get_libdir)/${PN}
+	doins *.txt || die
+	dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
+	echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > ${S}/99${PN}
+	doenvd "${S}/99${PN}" || die
+	dodoc Readmes/README.* || die
+}
diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/lagan/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>