reinit the tree, so we can have metadata

6 files changed, 163 insertions, 0 deletions

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<bool>(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<bool>(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 @@
+<?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>