sci-biology/seqan: SLOT 1.4 and 2.1, allow for parallel installation

Gentoo-Bug: 566502
* EAPI=6

Package-Manager: portage-2.2.28

5 files changed, 186 insertions, 0 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 134871573387..d7fdca839ecf 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,3 +1,4 @@
 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
+DIST seqan-src-2.1.1.tar.gz 110874831 SHA256 df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c SHA512 b82eb93129921eb867785add46d63f667c07f40556cd431acc73489c1032c19ff65b49415697415bdc7b788ffb8a80ab8d9e987fa38fc39c2399ff265fdc333f WHIRLPOOL b684d14db0cf22c7d1428c589293ee69674225e5b91845532f3135950a5a6178d4434b783177b3622e8661247856a20b42a7fb9275df4324124d2b21d728790f
diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
new file mode 100644
index 000000000000..4c7893e90c05
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
@@ -0,0 +1,30 @@
+Add default disabled flag to enable generation of documentation.
+For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
+support library for legacy tools.
+
+--- seqan-1.4.2/CMakeLists.txt
++++ seqan-1.4.2/CMakeLists.txt
+@@ -123,10 +123,12 @@
+ add_subdirectory (core)
+ message (STATUS "Configuring extras")
+ add_subdirectory (extras)
++if (NOT SEQAN_NO_DOX)
+ message (STATUS "Configuring docs")
+ add_subdirectory (docs)
+ message (STATUS "Configuring manual")
+ add_subdirectory (manual)
++endif ()
+ message (STATUS "Configuring sandbox")
+ add_subdirectory (sandbox)
+ message (STATUS "Configuring util/py_lib")
+--- seqan-1.4.2/docs/main.py
++++ seqan-1.4.2/docs/main.py
+@@ -123,7 +123,7 @@
+ 
+         # Done, print end message.
+         print 'Documentation created/updated.'
+-        return dddoc_html.WARNING_COUNT > 0
++        return 0
+     
+     
+ def main(argv):
diff --git a/sci-biology/seqan/files/seqan.pc.in b/sci-biology/seqan/files/seqan.pc.in
new file mode 100644
index 000000000000..f917faef8ba3
--- /dev/null
+++ b/sci-biology/seqan/files/seqan.pc.in
@@ -0,0 +1,10 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${prefix}
+includedir=${prefix}/include
+
+Name: @CMAKE_PROJECT_NAME@
+Description: C++ library for biological sequence analysis
+URL: http://www.seqan.de
+Version: @SEQAN_VERSION_STRING@
+Requires: zlib
+Cflags: -I${includedir}
diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
new file mode 100644
index 000000000000..28e6cad326d8
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils 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="$(get_version_component_range 1-2)"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse4_1 test"
+DEPEND="sys-libs/zlib
+	app-arch/bzip2
+	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1"
+
+#S="${WORKDIR}"/${PN}-${PN}-v${PV}
+
+PATCHES=(
+	"${FILESDIR}/${P}-shared.patch"
+	"${FILESDIR}/${P}-include.patch"
+	"${FILESDIR}/${P}-buildsystem.patch"
+)
+
+src_prepare() {
+	# pkg-config file, taken from seqan 2.1
+	cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die
+	sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \
+		-e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \
+		-e "s#@CMAKE_PROJECT_NAME@#${PN}#" \
+		-e "s#@SEQAN_VERSION_STRING@#${PV}#" \
+		-i ${PN}-${SLOT}.pc || die
+
+	rm -f util/cmake/FindZLIB.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBoost_NO_BOOST_CMAKE=ON
+		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+		-DSEQAN_NO_DOX=ON
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# SLOT header such that different seqan versions can be used in parallel
+	mkdir "${ED}"/usr/include/${PN}-${SLOT} || die
+	mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die
+
+	# pkg-config file
+	insinto /usr/share/pkgconfig/
+	doins ${PN}-${SLOT}.pc
+}
+
+pkg_postinst() {
+	einfo "${CATEGORY}/${PF} is only intended as support library for older"
+	einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop"
+	einfo "any new software against the latest SeqAn release and not this one."
+}
diff --git a/sci-biology/seqan/seqan-2.1.1.ebuild b/sci-biology/seqan/seqan-2.1.1.ebuild
new file mode 100644
index 000000000000..401b63c17525
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.1.1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils 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="$(get_version_component_range 1-2)"
+LICENSE="BSD GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cpu_flags_x86_sse4_1 doc test"
+DEPEND="sys-libs/zlib
+	app-arch/bzip2
+	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1"
+
+S="${WORKDIR}"/${PN}-${PN}-v${PV}
+
+src_prepare() {
+	# install docs in proper Gentoo structure
+	sed -e "s#share/doc/seqan#share/doc/${PF}#" \
+		-e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \
+		-i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die
+
+	# cmake module
+	sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${SLOT}\"#" \
+		-e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \
+		-e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${SLOT})#" \
+		-i util/cmake/FindSeqAn.cmake || die
+
+	# pkg-config file
+	sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \
+		-i util/pkgconfig/${PN}.pc.in || die
+
+	rm -f util/cmake/FindZLIB.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBoost_NO_BOOST_CMAKE=ON
+		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+		-DSEQAN_NO_DOX="$(usex !doc)"
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	cd "${BUILD_DIR}" || die
+	use doc && emake dox
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# SLOT header such that different seqan versions can be installed in parallel
+	mkdir "${ED}"/usr/include/${PN}-${SLOT} || die
+	mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die
+
+	# pkg-config file
+	mv "${ED}"/usr/share/pkgconfig/${PN}-{$(get_version_component_range 1),${SLOT}}.pc || die
+
+	dosym /usr/share/pkgconfig/${PN}-{${SLOT},$(get_version_component_range 1)}.pc
+}