diff options
Diffstat (limited to 'sci-chemistry/vmd')
| -rw-r--r-- | sci-chemistry/vmd/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-chemistry/vmd/Manifest | 12 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch | 25 | ||||
| -rw-r--r-- | sci-chemistry/vmd/metadata.xml | 22 | ||||
| -rw-r--r-- | sci-chemistry/vmd/vmd-1.9.1-r2.ebuild | 228 |
5 files changed, 279 insertions, 18 deletions
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog index 70ce782d4252..cf71b1078870 100644 --- a/sci-chemistry/vmd/ChangeLog +++ b/sci-chemistry/vmd/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/vmd -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.52 2012/11/29 15:13:06 jlec Exp $ +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.53 2013/01/11 09:29:35 jlec Exp $ + +*vmd-1.9.1-r2 (11 Jan 2013) + + 11 Jan 2013; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r2.ebuild, + +files/vmd-1.9.1-tcl8.6.patch, metadata.xml: + Use cuda.eclass and slo-operator for tcl 29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1.ebuild, vmd-1.9.1-r1.ebuild: diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index 1ca3c0fddb16..0d39c0705285 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,17 +1,19 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 +AUX vmd-1.9.1-tcl8.6.patch 1218 SHA256 41c1c3edf77f8ffcf8b7533625471d2dc384ca9a86ab9ba6be8d083718836b33 SHA512 ef729ddadbb865024abd6a532c328fe33e667faf0a6f9b09e3fcac852c2d88713b9efce772c42549fd62e9194634e3467d76700d0d317a1bd852be7baee8c125 WHIRLPOOL 9c122bb56fa66a1dffc6aa27d3e28bcf4848c3baf8a34a048fce3c2888a5ddfc6a92a5e8f9f1fa113b19c4b7d622d290be0e5cdafaae9d0a72402ef26143aa9f DIST vmd-1.9.1-gentoo-patches-2.tar.xz 79212 SHA256 1249957baea6fc8d4c05b008362b185b0851d70c6eeed8fbd44d41e7e77f23a8 SHA512 b313ed92652a93647790d668bd71233708fec3e9cead8b13b31dee1277f5ef6f0e8844f563ad51bc320b83a3cda126f8ab74fe4147218c65b594ee5624b46057 WHIRLPOOL 51b8a1486c286c002d893ec4e3aa8301ec7da6b9f2de31e880c7f9523a006a06712adecd5329269c892764761da691a36e1d6e5a730fc1a32c751b7658b96903 DIST vmd-1.9.1-gentoo-patches.tar.xz 79240 SHA256 60fe1b017b1aed5cdd4a417d4a2dbd20f75eae24c83d1da68c504a31bfbdbcd8 SHA512 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5dc98a0406e02fa9d271878afc532df0b749cb9f66ee40e6e83be066080aa2db2905cdee35ce1b0a5f8c67e3c151958149d42adc2f1c3985d90dd1bcb8ce39fc WHIRLPOOL 6a6bc8c76396d22a9653073235396ac2d02082691bb0d074f6c0697e87821ca35ecb0fe868c2ad680c7e5d6a4b9740d6a11d2b47d400cadca255675597ad2b46 -MISC metadata.xml 580 SHA256 ed78f23bbbbf847e14f5c62b82f2ddce852381ed344a5c09f2f1722ea60d6ebe SHA512 d5160cc475cc1d44a519413d570af32f58463e5469e932eb371a838ad5aed87ebeb380cfd1dcac5b9a3bb98e58d70fdd7d4f89a8ec7e649930b990613cda2bd8 WHIRLPOOL 0871e8e3ebe39ef9e4fda2e5c1d2635aab72ee311ea0baf5d22d474bcf20424a954592937907d0a624c8697541ef7ebd6474e5d95f0fe4e1bf46431462537a2e +MISC ChangeLog 9355 SHA256 c67a8b1adccc6065de673b34684b9e2827e5879ae80d0608cf22121833b23dda SHA512 ad80027f94365ded82d393c5f436320d6b906b27113f83cacb1cf58197b09b44bfca6843421fba531b4b0f569a71f29e526b4823454e93dc1bcb04ec87e732d9 WHIRLPOOL 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b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch @@ -0,0 +1,25 @@ + plugins/molfile_plugin/src/webpdbplugin.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/plugins/molfile_plugin/src/webpdbplugin.c b/plugins/molfile_plugin/src/webpdbplugin.c +index 80b3bb9..78597f5 100644 +--- a/plugins/molfile_plugin/src/webpdbplugin.c ++++ b/plugins/molfile_plugin/src/webpdbplugin.c +@@ -202,7 +202,7 @@ static void *open_file_read(const char *filename, const char *filetype, + sprintf(url, "http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s",filename); + sprintf(cmd, "set token [::http::geturl \"%s\"]", url); + if (Tcl_Eval(interp, cmd) != TCL_OK) { +- fprintf(stderr, "Error loading PDB: %s\n",interp->result); ++ fprintf(stderr, "Error loading PDB: %s\n",Tcl_GetStringResult(interp)); + Tcl_DeleteInterp(interp); + return NULL; + } +@@ -211,7 +211,7 @@ static void *open_file_read(const char *filename, const char *filetype, + + result = Tcl_GetVar2(interp, (char *)"state", "body", TCL_GLOBAL_ONLY); + if (!result) { +- fprintf(stderr, "Error loading PDB: %s\n", interp->result); ++ fprintf(stderr, "Error loading PDB: %s\n", Tcl_GetStringResult(interp)); + Tcl_DeleteInterp(interp); + return NULL; + } diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml index be76141a652b..b9b5a0649de6 100644 --- a/sci-chemistry/vmd/metadata.xml +++ b/sci-chemistry/vmd/metadata.xml @@ -1,15 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> - </maintainer> - <herd>sci-chemistry</herd> - <use> - <flag name="msms">Add support for MSMS SAS calcualtion tool</flag> - <flag name="povray">Add support for povray raytracer for HQ images</flag> - <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag> - <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> - </use> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <herd>sci-chemistry</herd> + <use> + <flag name="msms">Add support for MSMS SAS calcualtion tool</flag> + <flag name="povray">Add support for povray raytracer for HQ images</flag> + <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag> + <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild new file mode 100644 index 000000000000..f87ef5f3b73d --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild @@ -0,0 +1,228 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild,v 1.1 2013/01/11 09:29:35 jlec Exp $ + +EAPI=5 + +PYTHON_DEPEND="2" + +inherit cuda eutils multilib prefix python toolchain-funcs + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz + ${P}.src.tar.gz" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda msms povray tachyon xinerama" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.5:0=[-truetype] + dev-lang/perl + dev-python/numpy + sci-libs/netcdf + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + cuda? ( + >=dev-util/nvidia-cuda-toolkit-3.1 + || ( + sys-devel/gcc:4.4 + sys-devel/gcc:4.5 ) + ) + xinerama? ( x11-libs/libXinerama )" +DEPEND="${CDEPEND} + dev-lang/swig" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) + tachyon? ( media-gfx/tachyon )" + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" + +pkg_nofetch() { + elog "Please download ${P}.src.tar.gz from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches-2.tar.xz" + elog "Place both in ${DISTDIR}" +} + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + use cuda && cuda_sanitize + + cd "${WORKDIR}"/plugins + + epatch \ + "${WORKDIR}"/${P}-gentoo-plugins.patch \ + "${FILESDIR}"/${P}-tcl8.6.patch + + [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o\":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o\":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" + + epatch "${WORKDIR}"/${P}-gentoo-base.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + +# local NUMPY_INCLUDE="numpy/core/include" +# sed -e "s:gentoo-python-include:${EPREFIX}$(python_get_includedir):" \ +# -e "s:gentoo-python-lib:${EPREFIX}$(python_get_libdir):" \ +# -e "s:gentoo-python-link:$(PYTHON):" \ +# -e "s:gentoo-numpy-include:${EPREFIX}$(python_get_sitedir)/${NUMPY_INCLUDE}:" \ +# -i configure || die "failed setting up python" + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" +} + +src_configure() { + local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" +# use tachion && myconf+=" LIBTACHYON" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="${EPREFIX}$(python_get_libdir)" \ + PYTHON_LIBRARY="$(python_get_library -l)" \ + NUMPY_INCLUDE_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" + + ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins + + emake \ + TCLINC="-I${EPREFIX}/usr/include" \ + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \ + NETCDFLIB="$(pkg-config --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" \ + NETCDFINC="$(pkg-config --cflags-only-I netcdf) ${EPREFIX}/usr/include" \ + NETCDFLDFLAGS="$(pkg-config --libs netcdf)" \ + LINUX + + # build vmd + cd "${S}"/src + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src + emake install + + # install docs + cd "${S}" + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} |