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-chemistry/autodock/Manifest | 6 ++ sci-chemistry/autodock/autodock-4.2.6.ebuild | 101 +++++++++++++++++++++ .../files/autodock-4.2.6-buildsystem.patch | 44 +++++++++ sci-chemistry/autodock/metadata.xml | 8 ++ 4 files changed, 159 insertions(+) create mode 100644 sci-chemistry/autodock/Manifest create mode 100644 sci-chemistry/autodock/autodock-4.2.6.ebuild create mode 100644 sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch create mode 100644 sci-chemistry/autodock/metadata.xml (limited to 'sci-chemistry/autodock') diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest new file mode 100644 index 000000000000..1d8ebab45df7 --- /dev/null +++ b/sci-chemistry/autodock/Manifest @@ -0,0 +1,6 @@ +AUX autodock-4.2.6-buildsystem.patch 1500 SHA256 4ff8d1c05f2dcb61edc36b82a13e3542f27b06b8d53e6939866b481da1f38155 SHA512 08a7643e2973f2ebdd01c54acb1e3e0802ea3d7a33cbed4c03f58d29c7e13a246418feb4a61088dae18c3ab78db6fd5b3c11f9974dec59fe46dbf7cfbbe98c3a WHIRLPOOL bfb4ff1ce12a2fe3f841043a4413f9bb42f828e665a67914dd75e4f7b2be0cea8e98649f9596c494d8cd45baa7177b03ef0540acc4068ee0085741750c4260c2 +DIST autodocksuite-4.2.6-src.tar.gz 35438010 SHA256 4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb WHIRLPOOL 18230783d13c2d82ad6427711a48dec0c6695301a52dcf419cf4feefb0b5f41bac5de53824313e75d9040ac8623915ba266e764e92ecad9869d845053ec60b93 +EBUILD autodock-4.2.6.ebuild 2178 SHA256 33b86ac589ad95502ff32dcba4bf67397ed81fbab8c6d9ab7a1decc5f857e7c6 SHA512 f8b186454cec3e7deb6078cfa659d15eeebdc7e4bcb36d03327603ecda063b8a383a032001b8db9ad849dddb2c5992ec57c4f0bb6d8031a89cdad44fb3d82acb WHIRLPOOL de4f8b0ef5da206b52a69e03db0909693ca524700aaf7a1beced43e6ebbe556252e16a7464c0d1b97e4af95299e1780a068e040803c022190ba29ecad4533a96 +MISC ChangeLog 2506 SHA256 f2fbd31d2ccda5afbbf4b84bef834b8cfe32808361e569cd9fc9e431fcfae230 SHA512 e48184516de00a54b87402a3d164ffc0630b9c732ce75e527435180fbfcebb8c9f2c2749770fed1baee43cd0d615ad40ff5efde7e2934fbb56089a3f01cec745 WHIRLPOOL d7431d9d8ef285e01914015bd4cf2c83a51aaf7c43c4781e6a882075d6d8f54c6c1d83753bcf8120ff0490be41aeced741cecee2023e6d1dc99f9393e9ada4c5 +MISC ChangeLog-2015 1951 SHA256 a50f671c0007f340554e37ec4cedadf54088746b7e061a4105a89311470c8b32 SHA512 8127922c5acd3b9a24e4ad496bded17b0f1d7575ffad2cc308182730e5a0b69db9f4838f22345ac9807666ce43935dcbd3d8a3020a8a178ce92ce5c339090ecd WHIRLPOOL 9e0822256de0dbf4fd418d22f8b485da54268c242e6796afc13368b5758483596079588d33e83defebbe942de5f5ff9211c8405c996eca753f287fb5daa7d7db +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild new file mode 100644 index 000000000000..862cda1437b9 --- /dev/null +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils python-any-r1 versionator + +MY_PN="autodocksuite" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A suite of automated docking tools" +HOMEPAGE="http://autodock.scripps.edu/" +SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples openmp test" + +RDEPEND="" +DEPEND="test? ( ${PYTHON_DEPS} )" + +S="${WORKDIR}/src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_prepare() { + local i + + epatch "${PATCHES[@]}" + + sed \ + -e "s/\tcsh/\tsh/" \ + -i auto{dock,grid}/Makefile.am || die + for i in autodock autogrid; do + pushd $i &>/dev/null + eautoreconf + popd &>/dev/null + done +} + +src_configure() { + local i + for i in autodock autogrid; do + pushd $i &>/dev/null + econf $(use_enable openmp) + popd &>/dev/null + done +} + +src_compile() { + emake -C autodock + emake -C autogrid +} + +src_test() { + elog "Testing autodock" + cd "${S}/autodock/Tests" || die + cp ../*.dat . || die + ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." + einfo "Testing autogrid" + cd "${S}/autogrid/Tests" || die + ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." +} + +src_install() { + if use openmp; then + newbin autodock/autodock4.omp ${PN}4 + dobin autogrid/autogrid4 + else + dobin autodock/autodock4 autogrid/autogrid4 + fi + + insinto /usr/share/${PN} + doins -r \ + autodock/{AD4_parameters.dat,AD4_PARM99.dat} \ + $(usex examples "autodoc/EXAMPLES" "") + + DOCS=( + RELEASENOTES + autodock/{AUTHORS,README} + autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc + autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf + ) + einstalldocs +} + +pkg_postinst() { + elog "The AutoDock development team requests all users to fill out the" + elog "registration form at:" + echo + elog "\thttp://autodock.scripps.edu/downloads/autodock-registration" + echo + elog "The number of unique users of AutoDock is used by Prof. Arthur J." + elog "Olson and the Scripps Research Institude to support grant" + elog "applications." +} diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch new file mode 100644 index 000000000000..ae44ffeb3159 --- /dev/null +++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch @@ -0,0 +1,44 @@ + src/autodock/Makefile.am | 6 +++--- + src/autogrid/Makefile.am | 4 ++-- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am +index 799a3c4..911897b 100644 +--- a/src/autodock/Makefile.am ++++ b/src/autodock/Makefile.am +@@ -459,7 +459,8 @@ endif + + BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h + +-AM_CXXFLAGS = -O3 # Agressive optimization ++AM_CXXFLAGS = ++#AM_CXXFLAGS = -O3 # Agressive optimization + #AM_CXXFLAGS = -g # debug + + # if gnu c++ compiler +@@ -488,8 +489,7 @@ endif + AM_CPPFLAGS = -DNOSQRT \ + -DUSE_DOUBLE \ + -DUSE_8A_NBCUTOFF \ +- -DUSE_INT_AS_FOURBYTELONG \ +- -O3 ++ -DUSE_INT_AS_FOURBYTELONG + # AM_LDFLAGS = -g # -g is MP debug + + +diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am +index b531099..b78b380 100644 +--- a/src/autogrid/Makefile.am ++++ b/src/autogrid/Makefile.am +@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \ + BUILT_SOURCES = default_parameters.h + + +-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization ++AM_CFLAGS = -Wall # All warnings, Agressive optimization + +-AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization ++AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization + AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling + # M Pique - add USE_8A_NBCUTOFF + AM_CPPFLAGS += -DUSE_8A_NBCUTOFF diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/autodock/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + -- cgit v1.2.3