From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QmPJA-0006jE-Tn for garchives@archives.gentoo.org; Thu, 28 Jul 2011 12:03:21 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 97E9C21C042; Thu, 28 Jul 2011 12:03:12 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 5D0CE21C042 for ; Thu, 28 Jul 2011 12:03:12 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id CF1E21B4017 for ; Thu, 28 Jul 2011 12:03:11 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 0BBA78003D for ; Thu, 28 Jul 2011 12:03:11 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/ambertools/ambertools-1.5-r1.ebuild X-VCS-Directories: sci-chemistry/ambertools/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: af2d23a6e79abd8092230d1045f9f689a776589b Date: Thu, 28 Jul 2011 12:03:11 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 166f589550e53356ff58cda551673b04 commit: af2d23a6e79abd8092230d1045f9f689a776589b Author: Alexey Shvetsov gentoo org> AuthorDate: Thu Jul 28 12:02:48 2011 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Thu Jul 28 12:02:48 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Daf2d23a6 [sci-chemistry/ambertools] Updates for ambertools and gcc-4.6 (Portage version: 2.2.0_alpha47/git/Linux x86_64, signed Manifest commit = with key F82F92E6) --- sci-chemistry/ambertools/ambertools-1.5-r1.ebuild | 140 +++++++++++++++= ++++++ 1 files changed, 140 insertions(+), 0 deletions(-) diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chem= istry/ambertools/ambertools-1.5-r1.ebuild new file mode 100644 index 0000000..bebe615 --- /dev/null +++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild @@ -0,0 +1,140 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3D4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION=3D"A suite for carrying out complete molecular mechanics inv= estigations" +HOMEPAGE=3D"http://ambermd.org/#AmberTools" +SRC_URI=3D" + AmberTools-${PV}.tar.bz2 + mirror://gentoo/${P}-bugfix_1-10.patch.xz" + +LICENSE=3D"GPL-2" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"mpi openmp X" + +RESTRICT=3D"fetch" + +RDEPEND=3D" + virtual/cblas + virtual/lapack + sci-libs/clapack + sci-libs/arpack + sci-libs/cifparse-obj + sci-chemistry/mopac7 + sci-libs/netcdf + sci-libs/fftw:2.1 + sci-chemistry/reduce + virtual/fortran" +DEPEND=3D"${RDEPEND} + dev-util/byacc + dev-libs/libf2c + sys-devel/ucpp" +S=3D"${WORKDIR}/amber11" + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "Place it in ${DISTDIR}" +} + +pkg_setup() { + fortran-2_pkg_setup + if use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi + AMBERHOME=3D"${S}" +} + +src_prepare() { + epatch \ + "${WORKDIR}/${P}-bugfix_1-3.patch" \ + "${FILESDIR}/${P}-gentoo.patch" + cd AmberTools/src + rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf= reduce ucpp-1.3 || die +} + +src_configure() { + cd AmberTools/src + sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ + -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g"= \ + -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ + -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfft= w.a:g" \ + -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw= .a:g" \ + -e "s:CFLAGS=3D:CFLAGS=3D${CFLAGS} -DBINTRAJ :g" \ + -e "s:FFLAGS=3D:FFLAGS=3D${FFLAGS} :g" \ + -e "s:LDFLAGS=3D$ldflags:LDFLAGS=3D${LDFLAGS}:g" \ + -e "s:fc=3Dg77:fc=3D$(tc-getFC):g" \ + -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ + -e "s:NETCDF=3D\$netcdf:NETCDF=3Dnetcdf.mod:g" \ + -e "s:-O3::g" \ + -i configure || die + sed -e "s:arsecond_:arscnd_:g" \ + -i sff/time.c \ + -i sff/sff.h \ + -i sff/sff.c || die + sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ + -i nss/Makefile || die + + local myconf + + use X || myconf=3D"${myconf} -noX11" + + for x in mpi openmp; do + use ${x} && myconf=3D"${myconf} -${x}" + done + + ./configure \ + ${myconf} \ + -nobintraj \ + -nomdgx \ + -nopython \ + -nomtkpp \ + gnu +# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)') +} + +src_compile() { + cd AmberTools/src + emake || die +} + +src_install() { + rm -r bin/chemistry bin/MMPBSA_mods + rm bin/ante-MMPBSA.py bin/extractFrcmod.py + for x in bin/* + do dobin ${x} || die + done + rm "${ED}/usr/bin/yacc" + dobin AmberTools/src/antechamber/mopac.sh + sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ + -i "${ED}/usr/bin/mopac.sh" || die + # Make symlinks untill binpath for amber will be fixed + dodir /usr/share/${PN}/bin + cd "${ED}/usr/bin" + for x in * + do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} + done + cd "${S}" +# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \ +# -i "${ED}/usr/bin/xleap" \ +# -i "${ED}/usr/bin/tleap" || die + dodoc doc/AmberTools.pdf doc/leap_pg.pdf + dolib.a lib/* + insinto /usr/include/${PN} + doins include/* + insinto /usr/share/${PN} + doins -r dat + cd AmberTools + doins -r benchmarks + doins -r examples + doins -r test + cat >> "${T}"/99ambertools <<- EOF + AMBERHOME=3D"${EPREFIX}/usr/share/ambertools" + EOF + doenvd "${T}"/99ambertools +}