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, 210 insertions, 0 deletions

diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
new file mode 100644
index 000000000000..fd4e75d3fee9
--- /dev/null
+++ b/sci-biology/glimmerhmm/Manifest
@@ -0,0 +1 @@
+DIST GlimmerHMM-3.0.1.tar.gz 45475952 SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 WHIRLPOOL f2cc0f6cea083c223273dd59f9474a054c049b697fc122925d4f5820170ade67bfa76c6dd218ab10be5675fe0a2a2a9fa5172be540509770332cc5a1d6862ff7
diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
new file mode 100644
index 000000000000..949a4fe3e92d
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch
@@ -0,0 +1,153 @@
+ sources/makefile |   15 +++++--------
+ train/makefile   |   59 +++++++++++++++++++++++++++++++----------------------
+ 2 files changed, 40 insertions(+), 34 deletions(-)
+
+diff --git a/sources/makefile b/sources/makefile
+index f287d71..c560f48 100644
+--- a/sources/makefile
++++ b/sources/makefile
+@@ -2,25 +2,22 @@
+ 
+ 
+ 
+-CC=g++
+-CFLAGS=-g
+-
+ all: glimmerhmm
+ 
+ glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
+-	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
+ 
+ glimmerhmm.o: glimmerhmm.c
+-	$(CC) $(CFLAGS) -c glimmerhmm.c
++	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
+ 
+ graph.o: graph.c 
+-	$(CC) $(CFLAGS) -c graph.c
++	$(CXX) $(CXXFLAGS) -c graph.c
+ 
+ sites.o: sites.c
+-	$(CC) $(CFLAGS) -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
+ 
+ tree_util_prob.o: tree_util_prob.c
+-	$(CC) $(CFLAGS) -c tree_util_prob.c
++	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
+ 
+ util.o: util.c
+-	$(CC) $(CFLAGS) -c util.c
++	$(CXX) $(CXXFLAGS) -c util.c
+diff --git a/train/makefile b/train/makefile
+index 2383f18..d5a7107 100644
+--- a/train/makefile
++++ b/train/makefile
+@@ -2,9 +2,6 @@
+ 
+ # C compiler
+ 
+-C       = gcc 
+-CC      = g++ 
+-CFLAGS  = -O1 ${SEARCHDIRS}
+ #CFLAGS  = -O3 -g -Wall
+ LIBS    = -lm
+ 
+@@ -15,64 +12,76 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
+ 
+ 
+ misc.o: misc.c
+-	${C} ${CFLAGS} -c misc.c
++	$(CC) $(CFLAGS) -c misc.c
+ 
+ build-icm.o: build-icm.c
+-	${C} ${CFLAGS} -c build-icm.c
++	$(CC) $(CFLAGS) -c build-icm.c
+ 
+ build-icm: build-icm.o misc.o
+-	$(C) -o $@ build-icm.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
+ 
+ build-icm-noframe.o: build-icm-noframe.c
+-	${C} ${CFLAGS} -c build-icm-noframe.c
++	$(CC) $(CFLAGS) -c build-icm-noframe.c
+ 
+ build-icm-noframe: build-icm-noframe.o misc.o
+-	$(C) -o $@ build-icm-noframe.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
+ 
+ build1: build1.o
+-	${CC} build1.c -o build1 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS)
+ 
+ build2: build2.o
+-	${CC} build2.c -o build2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS)
+ 
+ falsecomp: falsecomp.o
+-	${CC} falsecomp.c -o falsecomp $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS)
+ 
+ findsites: findsites.o
+-	${CC} findsites.c -o findsites $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS)
+ 
+ karlin: karlin.o
+-	${CC} karlin.c -o karlin $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS)
+ 
+ score: score.o
+-	${CC} score.c -o score $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS)
+ 
+ score2: score2.o
+-	${CC} score2.c -o score2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS)
+ 
+ scoreATG: scoreATG.o
+-	${CC} scoreATG.c -o scoreATG $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS)
+ 
+ scoreATG2: scoreATG2.o
+-	${CC} scoreATG2.c -o scoreATG2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS)
+ 
+ scoreSTOP: scoreSTOP.o
+-	${CC} scoreSTOP.c -o scoreSTOP $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS)
+ 
+ escoreSTOP2: scoreSTOP2.o
+-	${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS)
+ 
+-rfapp: erfapp.o
+-	${CC} erfapp.c -o erfapp $(LIBS)
++erfapp: erfapp.o
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
+ 
+ sites.o: sites.c
+-	${CC} ${CFLAGS} -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
++
++scoreATG.o: scoreATG.c
++	$(CXX) $(CXXFLAGS) -c scoreATG.c
++	
++scoreSTOP.o: scoreSTOP.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
++
++scoreSTOP2.o: scoreSTOP2.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
++
++scoreATG2.o: scoreATG2.c
++	$(CXX) $(CXXFLAGS) -c scoreATG2.c
+ 
+ utils.o: utils.c 
+-	${CC} ${CFLAGS} -c utils.c
++	$(CXX) $(CXXFLAGS) -c utils.c
+ 
+ splicescore.o: splicescore.c
+-	${CC} ${CFLAGS} -c splicescore.c
++	$(CXX) $(CXXFLAGS) -c splicescore.c
+ 
+ splicescore: splicescore.o sites.o utils.o
+-	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
new file mode 100644
index 000000000000..bbddc6bdc8ad
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="A eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+src_unpack() {
+	unpack ${A}
+	mv GlimmerHMM ${P}
+}
+
+src_prepare() {
+	sed \
+		-e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
+		-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
+		-i "${S}/train/trainGlimmerHMM" || die
+
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+	tc-export CC CXX
+}
+
+src_compile() {
+	emake -C "${S}/sources"
+	emake -C "${S}/train"
+}
+
+src_install() {
+	dobin sources/glimmerhmm train/trainGlimmerHMM
+
+	insinto /usr/share/${PN}/lib
+	doins train/*.pm
+	insinto /usr/share/${PN}/models
+	doins -r trained_dir/*
+	exeinto /usr/libexec/${PN}/training_utils
+	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+	dodoc README.first train/readme.train
+}
diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/glimmerhmm/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>