diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-chemistry/tinker |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-chemistry/tinker')
-rw-r--r-- | sci-chemistry/tinker/Manifest | 7 | ||||
-rw-r--r-- | sci-chemistry/tinker/files/7.1.2-openmp.patch | 15 | ||||
-rw-r--r-- | sci-chemistry/tinker/files/tinker-7.1.2-build.patch | 17 | ||||
-rw-r--r-- | sci-chemistry/tinker/metadata.xml | 8 | ||||
-rw-r--r-- | sci-chemistry/tinker/tinker-7.1.2.ebuild | 105 |
5 files changed, 152 insertions, 0 deletions
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest new file mode 100644 index 000000000000..a6f2060da5e8 --- /dev/null +++ b/sci-chemistry/tinker/Manifest @@ -0,0 +1,7 @@ +AUX 7.1.2-openmp.patch 400 SHA256 67cf53b3801814ab39b4bdbb40db9f500cbc4740e2b7db94a945829ef1961cec SHA512 1af405acc753d602501589725374e88964a55e5954cb77eb1f3c0156fa73936552be9ce5fc4f36c855dfbd4043f12749dfc95aa9b946d80d0e5e6e8100e84ad4 WHIRLPOOL 6f20e980f63f79d3443f46d5608ad241723b73026cc3ec85437cb741a1c2b7b3fe74de428097583f3f34ac05d85e14edfe0490a04d48cccfd64d4ded2850dfb2 +AUX tinker-7.1.2-build.patch 360 SHA256 26fba46b9a72407cfd194cf74d5044b06b41164ae039b0b97f29b1840be4f765 SHA512 b20a4d8e75a781cd9c769dd0b5ae4e1039ea54d7ac61fc3605543b796afa2f4f3957be439f338fd47090a17e9153a466c2f76b364f4d9b7a2705b746f6cefbd3 WHIRLPOOL e102e8fafacc51160e191535355ae6fc7216c76b21234f6878c252eeebcb306bac8678413da26b44ff20a32b7652eda189eb66eb44efd577eb007e8685f8222f +DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46 +EBUILD tinker-7.1.2.ebuild 2275 SHA256 ddb245287de264e81e8c1ea7b0ef3749aaf9d218f49b6d165d3b1ecc41437c22 SHA512 d617f08cf03f35e78f0561214dcc0c7c4af0fedce69214a302ca8dee2c2a3577ba002671f4cce8a86cb3ca76084ce99eff6a2e90ecfc940c7aa56fd588edda2c WHIRLPOOL 6875ec865fd927d27c9fd5644da5b6a739f45e275f7e1a424a470e8610d5aa45e28ef03b5c200c6419e694928fc5841980c62c770cfe10c366a95d4ac9b1cf85 +MISC ChangeLog 2546 SHA256 40f1e60e2f001e8fc7c6cdb4c5effb89840a850c45347fe6e9e9fd74905ccd61 SHA512 fc9b14a4abb63367ae77af1c6eb7f49ac4169cb6df6250d5daa7b34559361860a6fda404976eacec50d0149c4b4d48eb59c45addf58e5133bcf9fb9be87e1588 WHIRLPOOL 107d50ddc5826ce1e19e9c9d47a1a7356b9aed04bcce26e95d73437215e5074a914320af789333ec4f1cfa6415277519d9191822b210265d353021e4bec125b7 +MISC ChangeLog-2015 5325 SHA256 628dfafc7626fc1bb8e814c00f4f80e559a5c14a539709499e196e848182c4cd SHA512 a8f802aca8a0e694569ddf5174d7a60c840435d11f745e705d9e381d93ebfdf636c6b790b9f02638b51101e28e688532f09566a6384ec83f7cc5d3af6bf34c86 WHIRLPOOL 81e4ec3bd16032f86598883c50e4a8e93123ef8f8394f8665d2268afbe154fd8b10178eb733188d11078d8f630662db048be7e105e953cd4b30ae90d59be9d38 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch new file mode 100644 index 000000000000..f3e8e2932b4a --- /dev/null +++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch @@ -0,0 +1,15 @@ +diff --git a/source/initial.f b/source/initial.f +index 835f228..4099c74 100644 +--- a/source/initial.f ++++ b/source/initial.f +@@ -73,8 +73,8 @@ c + c + c Intel compiler extensions to OpenMP standard + c +-!$ call kmp_set_stacksize_s (2**28) +-!$ call kmp_set_blocktime (0) ++! call kmp_set_stacksize_s (2**28) ++! call kmp_set_blocktime (0) + c + c values of machine precision constants + c diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch new file mode 100644 index 000000000000..d6ef484b19a4 --- /dev/null +++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch @@ -0,0 +1,17 @@ + make/Makefile | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/make/Makefile b/make/Makefile +index 61d5037..9be384a 100644 +--- a/make/Makefile ++++ b/make/Makefile +@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \ + %.x: %.o libtinker.a + ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ + +-all: +- ${EXEFILES} ++all: ${EXEFILES} + + install: + rename diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/tinker/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/tinker/tinker-7.1.2.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild new file mode 100644 index 000000000000..46a8d2feb0f2 --- /dev/null +++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs + +DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" +HOMEPAGE="http://dasher.wustl.edu/tinker/" +SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Tinker" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +DEPEND=" + >=virtual/jdk-1.6" + +RDEPEND=" + >=sci-libs/fftw-3.2.2-r1[fortran,threads] + dev-libs/maloc + !sys-apps/bar + !dev-util/diffuse + >=virtual/jre-1.6" + +RESTRICT="mirror" + +S="${WORKDIR}"/${PN}/source + +pkg_setup() { + fortran-2_pkg_setup + java-pkg-opt-2_pkg_setup + tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]" +} + +src_prepare() { + sed 's:strip:true:g' -i ../make/Makefile + [[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch + cd .. && epatch "${FILESDIR}"/${P}-build.patch +} + +src_compile() { + local javalib= + for i in $(java-config -g LDPATH | sed 's|:| |g'); do + [[ -f ${i}/libjvm.so ]] && javalib=${i} + done + + # use dummy routines in pmpb.f instead of apbs calls + rm pmpb.c || die + + if [[ $(tc-getFC) =~ "gfortran" ]]; then + append-flags -fopenmp + _omplib="-lgomp" + else + append-flags -openmp + _omplib="-liomp5" + fi + + _fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)" + + emake \ + -f ../make/Makefile \ + F77="$(tc-getFC)" \ + CC="$(tc-getCC) -c" \ + F77FLAGS=-c \ + OPTFLAGS="${FFLAGS}" \ + LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \ + INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \ + LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \ + all + + mkdir "${S}"/../bin || die + + emake \ + -f ../make/Makefile \ + BINDIR="${S}"/../bin \ + rename +} + +src_test() { + cd "${WORKDIR}"/${PN}/test/ + for test in *.run; do + einfo "Testing ${test} ..." + bash ${test} || die + done +} + +src_install() { + dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* + + insinto /usr/share/${PN}/ + doins -r "${WORKDIR}"/${PN}/params + + dodoc \ + "${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README} + + if use examples; then + insinto /usr/share/${P} + doins -r "${WORKDIR}"/${PN}/example + + doins -r "${WORKDIR}"/${PN}/test + fi + +} |