From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/express/Manifest | 9 ++++ sci-biology/express/express-0.9.5-r1.ebuild | 35 ++++++++++++++ sci-biology/express/express-1.5.1.ebuild | 37 +++++++++++++++ .../express/files/express-1.5.1-buildsystem.patch | 55 ++++++++++++++++++++++ sci-biology/express/files/express-1.5.1-gcc6.patch | 19 ++++++++ sci-biology/express/metadata.xml | 8 ++++ 6 files changed, 163 insertions(+) create mode 100644 sci-biology/express/Manifest create mode 100644 sci-biology/express/express-0.9.5-r1.ebuild create mode 100644 sci-biology/express/express-1.5.1.ebuild create mode 100644 sci-biology/express/files/express-1.5.1-buildsystem.patch create mode 100644 sci-biology/express/files/express-1.5.1-gcc6.patch create mode 100644 sci-biology/express/metadata.xml (limited to 'sci-biology/express') diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest new file mode 100644 index 000000000000..6bd37964dc72 --- /dev/null +++ b/sci-biology/express/Manifest @@ -0,0 +1,9 @@ +AUX express-1.5.1-buildsystem.patch 1956 SHA256 e4266c79b6d2c34e518cc57a9542543109bcc484511711492b146a7a49cb1187 SHA512 246788b75a7f40c825cc7bf811de2bd44607b7ccf139d7302480ed7faae441ec95d5a37aec7f04effb1e3e47ed774b08291321cd227b0fa79306969b39e93d54 WHIRLPOOL 195d13b46b3e9b3b651c3994148049f7c626dca395c2dbf1ca2eb5e8febb1b8d3d8ef501cd01a62fdc4a5a7a1236970fe6f644f9d5791d3b7fbbe28d7b58a7a3 +AUX express-1.5.1-gcc6.patch 722 SHA256 64be04111783bc1a38089d9a1b901f67c7499b894c51eb2e68b36b061fc0cfae SHA512 bbc7d7980bc88e241a76ad2b8a661ac8232f2cbc1a8cbf526b43905f9cdc52b57aadf8fb6bb03181b51893ac4e9d384ababb6d34582f7e24e6ef2ecc8fbfd73f WHIRLPOOL 9fa75d753b6432fb5e6bdb52ea54ba4d5fcf57fbade90ca2bb93c291c0807fc597d0844f7b6821822cd5b22d18060e3654d9b86ad9c5f1f544bcf9e9e4cbfedf +DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403 WHIRLPOOL 290772dceca2465f922f5d5fe548dc8fd460422589697173c58f98dc3afa2e91175fe1fa52e5f29458ea6af74c8da609776fa583bf5efcb2d5771c4c9ad51cde +DIST express-1.5.1-src.tgz 931166 SHA256 0c5840a42da830fd8701dda8eef13f4792248bab4e56d665a0e2ca075aff2c0f SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee WHIRLPOOL 2c75385b2a2ec8f7b77df760344affc108e827eb9f59014f08af0cee0ca8806beeba101d13ed8b43883a25fc9486bd405f402339f0e4e394d3895694c75a4e2a +EBUILD express-0.9.5-r1.ebuild 877 SHA256 b1242af3192914cbd60af84fa7fe9dd8809b11e4a8933ad5d2a39a2a4faac693 SHA512 6f3277de1bffa5855cf6db9c4733bb75420bc453f0feba464dacf51625d768ac23f3eb2ad3dd5de3389ae820371265085047d12224c08a05ced29d3b7f7cfe1f WHIRLPOOL a1e988c199a7bdbb5a2df654e3df22b160e973494e858893e832d5f8191ae8a115b4ebfcf479bdb4a0e433231eec58cb474d6684e58cf5fe6ba6eb14e47823e2 +EBUILD express-1.5.1.ebuild 737 SHA256 ceb5e7b903b346f8abe5f42d36b344885c654c4a0945c548b17673074f2d8bcc SHA512 23eb67f560b4b5ad76ecac73bab010a811363ae746c66cef13506e8fd2264f567bdcc283dc58face003bd3f63f077dbaf7d0b55616f50e2f55641a8beb58ceb0 WHIRLPOOL fa0e9212519a4baf133ed908209a2f25b99f14c4d83fa3ccc86a7c32d4e83a267281a41f7aa18d1940d9420cc0a66443a94c8541a62952b1efd41d09dc4dbb52 +MISC ChangeLog 2582 SHA256 c0df118069ef9ecd46ace790bf8ff2aeefb28e33b761c3cca7aefb532c4943de SHA512 571fe176297fed9f8fd2f01b1559416f471f7fb83dda5036fd5d7e082d8ed77feb51926f6aa9e414785da43ef3cf27ba219d5783ee71733f81c900169dce2b4c WHIRLPOOL 04a26d5096af267223c70e4416c76da60d897d3b7b3992788ef290699e2dbb7595dd2888a9d6a68b47d075c90ac057a1b0853a6a963e7532518c8806b6bc51d1 +MISC ChangeLog-2015 1224 SHA256 0bea782411fdecc57379bd8bc4958500ad4caa09ce82d4b0b7c2289f7a94d19a SHA512 816c7aa3f3d8936916c2e34cca498de37683558da6b8e3eb781240889dfffcd01c51939398b70ef835e76140d9c061c47a85142e0f96ba06067f8c7ae37e5c02 WHIRLPOOL 863134e26090629542ac08979f8f4f3c331481ca272b10cf63184c28dd9369452ede360c1db066abea748825fbeaa867ae8800fca5e518edc6fefb205fba670e +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/express/express-0.9.5-r1.ebuild b/sci-biology/express/express-0.9.5-r1.ebuild new file mode 100644 index 000000000000..945398a17a8f --- /dev/null +++ b/sci-biology/express/express-0.9.5-r1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild new file mode 100644 index 000000000000..62e5361f529f --- /dev/null +++ b/sci-biology/express/express-1.5.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + dev-libs/protobuf + dev-util/google-perftools + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch + "${FILESDIR}"/${P}-gcc6.patch +) + +src_configure() { + local mycmakeargs=( + -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools" + ) + cmake-utils_src_configure +} diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch new file mode 100644 index 000000000000..fca5feadd111 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch @@ -0,0 +1,55 @@ + CMakeLists.txt | 8 +++----- + src/CMakeLists.txt | 4 ++-- + 2 files changed, 5 insertions(+), 7 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index c768e28..65d5633 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) + set(${PROJECT_NAME}_VERSION_MINOR 5) + set(${PROJECT_NAME}_VERSION_PATCH 1) + +-set(CMAKE_CXX_FLAGS "-Wall") +- + set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") + + set(CMAKE_BUILD_TYPE Release) +-set(Boost_USE_STATIC_LIBS ON) ++set(Boost_USE_STATIC_LIBS OFF) + + find_package(Boost 1.39 + COMPONENTS +@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) + + find_package(Protobuf) + if (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 1) + else (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 0) + endif(PROTOBUF_FOUND) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 1cc0c01..8929d1f 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) + if(WIN32) + set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") + else(WIN32) +- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") ++ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") + endif(WIN32) + + if (PROTOBUF_FOUND) +- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") ++ set(LIBRARIES ${LIBRARIES} "protobuf") + endif(PROTOBUF_FOUND) + + target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch b/sci-biology/express/files/express-1.5.1-gcc6.patch new file mode 100644 index 000000000000..8a608b97b056 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-gcc6.patch @@ -0,0 +1,19 @@ +Bug: https://bugs.gentoo.org/610692 + +--- a/src/targets.cpp ++++ b/src/targets.cpp +@@ -113,12 +113,12 @@ + + double ll = LOG_1; + double tot_mass = mass(with_pseudo); +- double tot_eff_len = cached_effective_length(lib.bias_table); ++ double tot_eff_len = cached_effective_length(static_cast(lib.bias_table)); + if (neighbors) { + foreach (const Target* neighbor, *neighbors) { + tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); + tot_eff_len = log_add(tot_eff_len, +- neighbor->cached_effective_length(lib.bias_table)); ++ neighbor->cached_effective_length(static_cast(lib.bias_table))); + } + } + ll += tot_mass - tot_eff_len; diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/express/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + -- cgit v1.2.3