reinit the tree, so we can have metadata

8 files changed, 268 insertions, 0 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
new file mode 100644
index 000000000000..d84c49f908c6
--- /dev/null
+++ b/sci-biology/seqan/Manifest
@@ -0,0 +1,11 @@
+AUX seqan-1.4.2-buildsystem.patch 870 SHA256 d824d014400b94778ea427c6e6220813201c41ded9a0ec0fbe1aeb891b69a626 SHA512 d769eb4137c8c0ddb7137ecfdb0673ba8648ae720673848cbb473a0c80d479b6e5c564c12f1a9dd01953d955605eb2f273e04808ae50058c565e997381c3f748 WHIRLPOOL ba0447716248743c57b30c7cde6bd81b7af157c4a4b2249755e608861586b4f73f46799bf3c1070bfe84a67a532da1089796b032e01987a563a8395506bed661
+AUX seqan-1.4.2-include.patch 552 SHA256 fb97f772388de6de381c7214b8b5167b2079e19d7f839673e281537c4bc80516 SHA512 b02ab4fe49a511494134e44855d865f0ff210392810970834deb304499b5017764ed1c04d8f8dbfb513c333ac302946e5c72c9160cd38a5ef5ad095a865cb6d0 WHIRLPOOL 26a3278707276b95197192c140589a2cc95cd5d487144975219bf4d918884434b57186093595f92ec009679dc5eb912422520c245691da6e1cc3cc441c284a5b
+AUX seqan-1.4.2-shared.patch 974 SHA256 3c704fa149d0d4b322f8bb1b5536dafca35c205e5931a149fce5e82cac1dfe05 SHA512 a509c243244b6b40b26700a73be267558ceb17c4e0079f3eca606835ecfe8d1417b88fd37719ca9cf226e6d2d33ee3e22790b20e39a86a300f722eb186cabaad WHIRLPOOL eb7a76bb6c82e7a312356d0db13b6f90bd0fadc021ce1e62e8f2c8708f25a84911842df4df20a8491f5971d62fda5a738527d863bd10c2f1167fbed82cd00dea
+AUX seqan.pc.in 263 SHA256 54978d662cf1fcf4212e90d0b2681f2327476cfc0ebebef9cd3ab0b3b890c929 SHA512 bde1c89624284a37dac1a8717049a3b14340a2543003d9cf8406bddf4033541b65b617b802b18c80b2c7733d55ad9d7484bd85fdc927582363885da6d0210af7 WHIRLPOOL 6a901161d71ccf179b927c8c658a552b1f2dba1ef0bd63ee25f18e4dbeebd23a32d20729b07119f8eefd875e8809b6c56c79ed2cdf3f5c70c77b23a52aaa139c
+DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0
+DIST seqan-src-2.2.0.tar.gz 110936119 SHA256 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421 WHIRLPOOL 1241488ee52d315b6ca68ff730eb4d356db2102b8e78eb0be13cd9c07f0b04e96821a78944b3738204f67f08874cf328b0ef609b373cb8b077524b17b1e9650d
+EBUILD seqan-1.4.2-r1.ebuild 1961 SHA256 040fd7309a8b6328050d9bb981343dafc5f4b4a700df6dd17d7da7e7f2fd9462 SHA512 abbfc75ee90a12ffb200a02fb713dcd8098e040b79c2a204155a4e5c167966f829b17e6f5bc86752978f1ec2e0f84a474fbc77db49e4e44a6e5bd7bdbcfe6761 WHIRLPOOL 6d62b6a62c68df1ce730891b8487341fb9549854481119bdae1b1610983f69c34661c87f3f05e29ad47e2036a628e10300ad940a3d8f973338840a62f6fc2835
+EBUILD seqan-2.2.0-r1.ebuild 2667 SHA256 8d3b0fa351737038c1596dd29bedf66acd133e0cf4964116a10e599ad05aeece SHA512 6221563c1e5b4332d66f1524b856ef87da90aa730907c3e2427a7ab18493f381eeffc7ea506690131cfecc3f3f692eb447d008dede764cbd5b11475a738f0289 WHIRLPOOL fb86966d359cf982fb1671efe0950ba4ad30a1afe1834250de2eaae008a6a3354fb9e2fd5a2187016ef42ddd2a9c7cb03f8cceaa8241eee2074193a3933afca9
+MISC ChangeLog 4099 SHA256 21ecc5e9e7db99412e4be313a63097a5b081df91329722e5d57e3db625627ca4 SHA512 93bc2a2b24ae8a84d45dcb2bfd3ad746913f0ab7d6883957e7ff3bff95994e2532ee9b08d59d186818ea86e21d9d39c203197bdcaeb306c340af1ec3ff533f81 WHIRLPOOL 10f701807471c698a5674cd1c4a04cc411b2551316a293b96affc9bc051278c6a46aaa0df34af60a79d89c2a1d161b54bb611de1433d1f44371887739859d7a6
+MISC ChangeLog-2015 1512 SHA256 68892efa58a06b8280c4f5695af5fa38a63f614fa321081efc2ae50ac132ce65 SHA512 e92d8bc043e9f7a9a1b4ae8ce81a07f228d2242425d346216a51f4086a7b9df1e6b7aabf2236f16ce665e36cbc9cc6913083b5a7e7db422052c3d44f1469710e WHIRLPOOL 26f302900373ff167adbe3ce18599acae05e3a2294701f02987d0e8016b01abbd6d3d5a138853ab5a762700b00a6d4b13aafdf1265e9e93051486a142bcd548d
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
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-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
new file mode 100644
index 000000000000..5baee4d8ebc0
--- /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 000000000000..0f438ff07bce
--- /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 "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
+ 
+     # enable static linkage for seqan apps
+-    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
+-      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
+-    endif ()
++#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
++#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
++#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
++#    endif ()
+ 
+     # Get all direct entries of the current source directory into ENTRIES.
+     file (GLOB ENTRIES
diff --git a/sci-biology/seqan/files/seqan.pc.in b/sci-biology/seqan/files/seqan.pc.in
new file mode 100644
index 000000000000..f917faef8ba3
--- /dev/null
+++ b/sci-biology/seqan/files/seqan.pc.in
@@ -0,0 +1,10 @@
+prefix=@CMAKE_INSTALL_PREFIX@
+exec_prefix=${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/metadata.xml b/sci-biology/seqan/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/seqan/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
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..5fd8f1ae8a14
--- /dev/null
+++ b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils python-any-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"
+REQUIRED_USE="cpu_flags_x86_sse4_1"
+
+RDEPEND="
+	app-arch/bzip2
+	sys-libs/zlib"
+DEPEND="
+	${RDEPEND}
+	test? (
+		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
+		${PYTHON_DEPS}
+	)"
+
+PATCHES=(
+	"${FILESDIR}/${P}-shared.patch"
+	"${FILESDIR}/${P}-include.patch"
+	"${FILESDIR}/${P}-buildsystem.patch"
+)
+
+pkg_setup() {
+	use test && python-any-r1_pkg_setup
+}
+
+src_prepare() {
+	# pkg-config file, taken from seqan 2.1
+	cp "${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-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
new file mode 100644
index 000000000000..2452ff0baea6
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils python-any-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 doc test"
+REQUIRED_USE="cpu_flags_x86_sse4_1"
+
+RDEPEND="
+	app-arch/bzip2
+	sys-libs/zlib
+	!!sci-biology/seqan:2.0
+	!!sci-biology/seqan:2.1
+	!!sci-biology/seqan:2.2"
+DEPEND="
+	${RDEPEND}
+	doc? (
+		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
+		${PYTHON_DEPS}
+	)
+	test? (
+		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
+		${PYTHON_DEPS}
+	)"
+
+S="${WORKDIR}"/${PN}-${PN}-v${PV}
+
+pkg_setup() {
+	if use test || use doc; then
+		python-any-r1_pkg_setup
+	fi
+}
+
+src_prepare() {
+	seqan_major_ver=$(get_version_component_range 1)
+	seqan_majorminor_ver=$(get_version_component_range 1-2)
+
+	# install docs in proper Gentoo structure
+	sed -e "s#share/doc/seqan#share/doc/${PF}#" \
+		-e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \
+		-i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die
+
+	# cmake module
+	sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \
+		-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-${seqan_majorminor_ver})#" \
+		-i util/cmake/FindSeqAn.cmake || die
+
+	# pkg-config file
+	sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \
+		-i util/pkgconfig/${PN}.pc.in || die
+
+	rm -f util/cmake/FindZLIB.cmake || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+		-DSEQAN_NO_DOX=$(usex !doc)
+	)
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# multi-version header such that different seqan versions can be installed in parallel
+	mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die
+	mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die
+
+	# pkg-config file
+	mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die
+
+	# create pkg-config symlink to restore default behaviour
+	dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc
+}