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

8 files changed, 223 insertions, 0 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
new file mode 100644
index 00000000000..13487157338
--- /dev/null
+++ b/sci-biology/seqan/Manifest
@@ -0,0 +1,3 @@
+DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b
+DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
+DIST seqan-src-2.0.0.tar.gz 115731415 SHA256 69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512 9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a WHIRLPOOL afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4
diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 00000000000..5baee4d8ebc
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch
@@ -0,0 +1,16 @@
+ core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
+index 4a6c2e6..8cc9a42 100644
+--- a/core/include/seqan/index/index_qgram_openaddressing.h
++++ b/core/include/seqan/index/index_qgram_openaddressing.h
+@@ -35,6 +35,8 @@
+ #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
+ 
++#include <smmintrin.h>
++
+ namespace SEQAN_NAMESPACE_MAIN
+ {
+ 
diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
new file mode 100644
index 00000000000..0f438ff07bc
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
@@ -0,0 +1,22 @@
+ util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
+index bcba2c0..d53cd01 100644
+--- a/util/cmake/SeqAnBuildSystem.cmake
++++ b/util/cmake/SeqAnBuildSystem.cmake
+@@ -144,10 +144,10 @@ macro (seqan_register_apps)
+     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
new file mode 100644
index 00000000000..de14e9d58b8
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch
@@ -0,0 +1,15 @@
+ include/seqan/stream/zipstream/zutil.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/seqan/stream/zipstream/zutil.h b/include/seqan/stream/zipstream/zutil.h
+index 2806344..f8b41e6 100644
+--- a/include/seqan/stream/zipstream/zutil.h
++++ b/include/seqan/stream/zipstream/zutil.h
+@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */
+ 
+          /* functions */
+ 
++#define OF(x) x
+ #ifdef HAVE_STRERROR
+    extern char *strerror OF((int));
+ #  define zstrerror(errnum) strerror(errnum)
diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml
new file mode 100644
index 00000000000..f17a827e310
--- /dev/null
+++ b/sci-biology/seqan/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>
diff --git a/sci-biology/seqan/seqan-1.3.1-r1.ebuild b/sci-biology/seqan/seqan-1.3.1-r1.ebuild
new file mode 100644
index 00000000000..a74eac3ccfc
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.3.1-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://ftp.seqan.de/releases/${P}.zip"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${P}/cmake
+
+src_prepare() {
+	append-cppflags -I"${EPREFIX}/usr/include/bam"
+	rm -rf "${S}"/../lib/samtools || die
+
+	sed \
+		-e "s:docs:docs/.:g" \
+		-e "/DESTINATION/s:seqan:doc/${PF}/html:g" \
+		-i CMakeLists.txt || die
+
+	sed \
+		-e "/DESTINATION/s:bin):share/${PN}):g" \
+		-i apps/CMakeLists.txt || die
+
+	cmake-utils_src_prepare
+}
diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild
new file mode 100644
index 00000000000..a7e436a2013
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-shared.patch
+	"${FILESDIR}"/${P}-include.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} = "binary" ]] && return 0
+	if use amd64; then
+		if ! echo "#include <smmintrin.h>" | gcc -E - 2>&1 > /dev/null; then
+			ewarn "Need at least SSE4.1 support"
+			die "Missing SSE4.1 support"
+		fi
+	fi
+}
+
+src_prepare() {
+	rm -f \
+		util/cmake/FindZLIB.cmake \
+		|| die
+	touch extras/apps/seqan_flexbar/README || die
+	sed \
+		-e "s:share/doc:share/doc/${PF}:g" \
+		-i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBoost_NO_BOOST_CMAKE=ON
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	mkdir -p "${BUILD_DIR}"/docs/html || die
+	cmake-utils_src_install
+	chmod 755 "${ED}"/usr/bin/*sh || die
+
+	mv "${ED}"/usr/bin/{,seqan-}join || die
+}
+
+pkg_postinst() {
+	elog "Due to filecollision the 'join' binary has been renamed to seqan-join"
+}
diff --git a/sci-biology/seqan/seqan-2.0.0.ebuild b/sci-biology/seqan/seqan-2.0.0.ebuild
new file mode 100644
index 00000000000..5437e6df9f5
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.0.0.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils flag-o-matic python-single-r1
+
+DESCRIPTION="C++ Sequence Analysis Library"
+HOMEPAGE="http://www.seqan.de/"
+SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse4_1"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-libs/boost:=
+	sci-biology/samtools"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${PN}-${PN}-v${PV}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-zlib.patch
+)
+
+src_prepare() {
+	rm -f \
+		util/cmake/FindZLIB.cmake \
+		|| die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBoost_NO_BOOST_CMAKE=ON
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	mkdir -p "${BUILD_DIR}"/docs/html || die
+	cmake-utils_src_install
+	chmod 755 "${ED}"/usr/bin/*sh || die
+}