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, 107 insertions, 0 deletions

diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest
new file mode 100644
index 000000000000..acbb2140b6da
--- /dev/null
+++ b/sci-biology/vcftools/Manifest
@@ -0,0 +1 @@
+DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863
diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
new file mode 100644
index 000000000000..85197664a0d1
--- /dev/null
+++ b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
@@ -0,0 +1,53 @@
+diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile
+--- vcftools_0.1.12b.orig/cpp/Makefile	2014-08-01 21:11:22.000000000 +0200
++++ vcftools_0.1.12b/cpp/Makefile	2015-04-03 17:24:38.830781049 +0200
+@@ -3,8 +3,8 @@
+ # ($Revision: 1.1 $)
+ 
+ # Compiler
+-CC = gcc
+-CPP = g++
++CC ?= gcc
++CPP ?= g++
+ # Output executable
+ EXECUTABLE = vcftools
+ # Flag used to turn on compilation of PCA routines
+@@ -12,9 +12,9 @@
+ 	VCFTOOLS_PCA = 0
+ endif
+ # Compiler flags
+-CFLAGS = -O2 -m64
++CFLAGS ?= -O2 -m64
+ #CFLAGS = -Wall -O2 -pg -m64
+-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 
++CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 
+ #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
+ # Included libraries (zlib)
+ LIB = -lz 
+@@ -29,13 +29,13 @@
+ 	# Define flag for PCA routine compilation
+ 	CPPFLAGS += -DVCFTOOLS_PCA
+ 	# Add LAPACK library
+-	LIB += -llapack	
++	LIB += `$(PKG_CONFIG) --libs lapack`
+ 	# Add PCA source code
+ 	OBJS+= dgeev.o
+ endif
+ 
+ vcftools: $(OBJS)
+-	$(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB)
+ ifdef BINDIR
+ 	cp $(CURDIR)/$@ $(BINDIR)/$@
+ endif
+@@ -47,8 +47,8 @@
+ -include $(OBJS:.o=.d)
+ 
+ %.o: %.cpp
+-	$(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
+-	$(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
++	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o
++	$(CXX) -MM $(CXXFLAGS) $(CPPFLAGS)  $*.cpp > $*.d
+ 
+ # remove compilation products
+ clean:
diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml
new file mode 100644
index 000000000000..c45e9f4dea06
--- /dev/null
+++ b/sci-biology/vcftools/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="sourceforge">vcftools</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
new file mode 100644
index 000000000000..ddc214c430c0
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-buildsystem.patch
+	tc-export CXX PKG_CONFIG
+}
+
+src_compile() {
+	local myconf
+	use lapack && myconf="VCFTOOLS_PCA=1"
+	emake -C cpp ${myconf}
+}
+
+src_install(){
+	perl_set_version
+	dobin cpp/${PN}
+	insinto ${VENDOR_LIB}
+	doins perl/*.pm
+	dobin perl/{fill,vcf}-*
+	dodoc README.txt
+}