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sci-chemistry/autodock_vina: add 1.2.5
Signed-off-by: Alexey Shvetsov <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1,2 @@ | ||
| DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321 SHA512 d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9 | ||
| DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 |
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| @@ -0,0 +1,50 @@ | ||
| # Copyright 1999-2024 Gentoo Authors | ||
| # Distributed under the terms of the GNU General Public License v2 | ||
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| EAPI=7 | ||
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| inherit flag-o-matic toolchain-funcs | ||
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| MY_PN=AutoDock-Vina | ||
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| DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" | ||
| HOMEPAGE="http://vina.scripps.edu/" | ||
| SRC_URI="https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" | ||
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| S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release" | ||
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| LICENSE="Apache-2.0" | ||
| SLOT="0" | ||
| KEYWORDS="~amd64 ~x86" | ||
| IUSE="debug" | ||
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| RDEPEND="dev-libs/boost:=" | ||
| DEPEND="${RDEPEND}" | ||
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| PATCHES=( | ||
| "${FILESDIR}"/${P}-gentoo.patch | ||
| ) | ||
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| src_prepare() { | ||
| cd "${WORKDIR}/${MY_PN}-${PV}" || die | ||
| pwd | ||
| sed -e "s:VERSION:\"${PV}\":g" \ | ||
| -i src/main/main.cpp \ | ||
| -i src/split/split.cpp || die | ||
| default | ||
| } | ||
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| src_configure() { | ||
| append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14 | ||
| } | ||
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| src_compile() { | ||
| emake \ | ||
| BASE="${EPREFIX}"/usr/ \ | ||
| GPP="$(tc-getCXX)" \ | ||
| C_OPTIONS=$(usex debug '' -DNDEBUG) | ||
| } | ||
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| src_install() { | ||
| dobin vina{,_split} | ||
| } |
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sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-gentoo.patch
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,64 @@ | ||
| diff -urN AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile AutoDock-Vina-1.2.5/build/linux/debug/Makefile | ||
| --- AutoDock-Vina-1.2.5.orig/build/linux/debug/Makefile 2024-03-05 13:23:49.210511903 +0300 | ||
| +++ AutoDock-Vina-1.2.5/build/linux/debug/Makefile 2024-03-05 13:25:34.028499976 +0300 | ||
| @@ -1,7 +1,7 @@ | ||
| BASE=/usr | ||
| BOOST_VERSION= | ||
| BOOST_INCLUDE = $(BASE)/include | ||
| -C_PLATFORM=-static -pthread | ||
| +C_PLATFORM=-pthread | ||
| GPP=g++ | ||
| C_OPTIONS= -g -std=gnu++11 | ||
| BOOST_LIB_VERSION= | ||
| diff -urN AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile AutoDock-Vina-1.2.5/build/linux/release/Makefile | ||
| --- AutoDock-Vina-1.2.5.orig/build/linux/release/Makefile 2024-03-05 13:23:49.213845279 +0300 | ||
| +++ AutoDock-Vina-1.2.5/build/linux/release/Makefile 2024-03-05 13:26:10.285621339 +0300 | ||
| @@ -1,7 +1,7 @@ | ||
| BASE=/usr/local | ||
| BOOST_VERSION= | ||
| BOOST_INCLUDE = $(BASE)/include | ||
| -C_PLATFORM=-static -pthread | ||
| +C_PLATFORM=-pthread | ||
| GPP=g++ | ||
| C_OPTIONS= -O3 -DNDEBUG -std=c++11 | ||
| BOOST_LIB_VERSION= | ||
| diff -urN AutoDock-Vina-1.2.5.orig/build/makefile_common AutoDock-Vina-1.2.5/build/makefile_common | ||
| --- AutoDock-Vina-1.2.5.orig/build/makefile_common 2024-03-05 13:23:49.213845279 +0300 | ||
| +++ AutoDock-Vina-1.2.5/build/makefile_common 2024-03-05 13:28:30.557370911 +0300 | ||
| @@ -14,7 +14,7 @@ | ||
| #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) | ||
| CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS) | ||
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| -LDFLAGS = -L$(BASE)/lib -L. | ||
| +LDFLAGS = -L. | ||
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| # test if boost_thread-mt exists, this is | ||
| # necessary as some versions of boost only | ||
| @@ -32,22 +32,22 @@ | ||
| ifeq ($(BOOST_STATIC), y) | ||
| LIBS = ${BASE}/lib/libboost_system${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_thread${threadmt}${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_serialization${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_filesystem${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_program_options${BOOST_LIB_VERSION}.a | ||
| else | ||
| -LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread | ||
| +LIBS = -l boost_system -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options -l pthread | ||
| endif | ||
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| .SUFFIXES: .cpp .o | ||
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| %.o : ../../../src/lib/%.cpp | ||
| - $(CC) $(CFLAGS) -o $@ -c $< | ||
| + $(CC) $(CXXFLAGS) -o $@ -c $< | ||
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| %.o : ../../../src/design/%.cpp | ||
| - $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< | ||
| + $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< | ||
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| %.o : ../../../src/main/%.cpp | ||
| - $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< | ||
| + $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< | ||
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| %.o : ../../../src/split/%.cpp | ||
| - $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< | ||
| + $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< | ||
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| all: vina vina_split | ||
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