diff options
| -rw-r--r-- | sci-chemistry/vmd/Manifest | 2 | ||||
| -rw-r--r-- | sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild | 269 |
2 files changed, 271 insertions, 0 deletions
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index 584d38bd84a5..0cc49d841bd2 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,3 +1,5 @@ DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc +DIST vmd-1.9.4_alpha57-gentoo-patches.tar.xz 14612 BLAKE2B e50a2fc734038207174dd5cc525f01824ce324a65b8ce604f83862ce50be6b1950d199188a717e2368b2b050256a4705662009e3530d621b19c52bb109b6a844 SHA512 6283076e47dfcd780bbc94f9ca2b044a028a472c09d78616d373813d81ec764bf1697e56a8f487f9f0999cf409c0f141bf248156f60851073347d1b640a6953c DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40 DIST vmd-1.9.4a55.src.tar.gz 43049895 BLAKE2B 311fdbf8742647d1dbba8346e8559d26b19ec445bb5df4b23f684c5769997e2261e200b8118668d296654f59ab340fc150f5aa33fc808ad55f2e78ce7030960b SHA512 1be5f50555423120fd8c5c335a346a40253fb80cc352f08907d864f6b34d3debe28d9a3fbf821c3a6c7c86c615fd09735c05aadf1b4503722075e9ab0b946378 +DIST vmd-1.9.4a57.src.tar.gz 43155120 BLAKE2B de0da96f6681c24e7b1d38890f109088187198cbdddb3d86d783322e837b7a71224085699f3addf2833cf293ab2689f06ab47df284b8fbe080162740094ae844 SHA512 0a3726d8fa279ac62c368cd18724cd09535618454ff6e299d147291ef5d4198ad9d58a94f0b05699ec8a23128753c55e7397c95a5ce194e36d3fabef1bcf454c diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild new file mode 100644 index 000000000000..d4c354c5bd35 --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild @@ -0,0 +1,269 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +PYTHON_COMPAT=( python3_{8..10} ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" + +MY_PV="${PV/_alpha/a}" +MY_P="${PN}-${MY_PV}" +SRC_URI=" + ${MY_P}.src.tar.gz + fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz +" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +CDEPEND="${PYTHON_DEPS} + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + ') + >=dev-lang/tk-8.6.1:0= + dev-lang/perl + dev-libs/expat + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama ) +" +DEPEND="${CDEPEND}" +BDEPEND=" + virtual/pkgconfig + dev-lang/swig +" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/chemical-mime-data + sci-chemistry/surf + x11-misc/xdg-utils + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) +" + +S="${WORKDIR}/${MY_P}" + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" + +# Binary only plugin +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil" + +pkg_nofetch() { + elog "Please download ${MY_P}.src.tar.gz from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license." + elog "Place it into your DISTDIR directory." +} + +src_prepare() { + # Apply user patches from ${WORKDIR} to allow patching on patches + # subdir too + cd "${WORKDIR}" + default + + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch + + use cuda && cuda_sanitize + + # Prepare plugins + cd plugins || die + + 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}" || die + + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch + + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html + eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-tmpdir.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 $(fltk-config --libs)):g" \ + -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ + -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + 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 || die + 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-patches/vmd.png + eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop + domenu "${WORKDIR}"/vmd-patches/vmd.desktop +} |