diff options
Diffstat (limited to 'sci-chemistry')
42 files changed, 311 insertions, 473 deletions
diff --git a/sci-chemistry/chimera-bin/Manifest b/sci-chemistry/chimera-bin/Manifest deleted file mode 100644 index a3bee4f39..000000000 --- a/sci-chemistry/chimera-bin/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST chimera-1.14-linux_x86_64.bin 157644313 BLAKE2B 75dba07faa5cbd76b472318a50f8dc9dbedfccd9f2ff59769cb5517639d4381f025ecfc206a6c61bd1bfe49928d3bf9076e5506db2a7b700923663399657ac46 SHA512 2309305cff892e28b89d8281231c1546212143cc347885f83544a85f776733329ba6adc7dc748cb4453e31a6eb535b57487ecd34b1c1800ff222950e92109e85 -DIST chimera-1.15-linux_x86_64.bin 154069682 BLAKE2B 802f9e1b0182bf8b6ae38057145c25f2abfd2e71a3e4b7651a73130c8e11c9aee5e7eba230c2558821a95f33c6a4619897be355ee7ce3be0d319ded88a71b63f SHA512 7c4be169f22ab9557ac89087938a52b5c3d41d0971ff52e6ecf9c7dce41126f88a2c6f626e8b5c8876fe52fe36c94c55a61b515da7e7bdde17046546e75f4b97 diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/chimera-bin/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?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/chimera/Manifest b/sci-chemistry/chimera/Manifest new file mode 100644 index 000000000..953fae5f9 --- /dev/null +++ b/sci-chemistry/chimera/Manifest @@ -0,0 +1,3 @@ +DIST Chimera512.png 68464 BLAKE2B 51797728b8b9421ab6e42e57bb60881a706d17eed09cbef57506f706b7ebab6511397f90834d15efaea5e86a22fc2ff9e55cf42c7a87d6166716444252d18f49 SHA512 6ed0dd8bd1b5a6b164f80acc1d7e1a91629513b147d37472e1831b657201a3f25c1c0c9a1b44bf565afaa4aa99469910d1ac307a45a80b9a12d0554e1812e2c5 +DIST chimera-1.17.1-linux_x86_64.bin 149832020 BLAKE2B 01e78d09a3373a3d927c93daa03d0c17473c18079afd989a29afaad5c56aa57bbfeb968bcef42eb50924e1cde67e939c92a545080c0e7b55549c30e43aae564d SHA512 f6df3ad320f09b3f8d918660a4a7596505c2a97ac0d60a4f6ef9c414851a90bb59ccba9728d5a71df93404b8c6ecf99ab9dca84befcfa10e60285f3a33e3c3bc +DIST chimera-1.17.3-linux_x86_64.bin 155528316 BLAKE2B 09caddbac9a518606b8065a19840fd2f5e3a57cbb529bea2e4b63cb83ecd91105c1de34dc3f1139382fc80f14e69b28c39152d9b15e16c39a08732ebcd374c51 SHA512 cfbf42dd3aa030db0619bf5750d08ba94acc53f54a890109d422a675394616afba9c85779e5d62bcd4ad83db4a7cfcf8190c2c42c84719c991061859c87288b7 diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild b/sci-chemistry/chimera/chimera-1.17.1.ebuild index 7d5f9147a..919350ac9 100644 --- a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild +++ b/sci-chemistry/chimera/chimera-1.17.1.ebuild @@ -1,19 +1,23 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 - +EAPI=8 inherit desktop xdg -DESCRIPTION="An extensible Molecular Modelling System" +DESCRIPTION="Next generation molecular visualization program from RBVI" HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" -SRC_URI="chimera-${PV}-linux_x86_64.bin" +SRC_URI="chimera-${PV}-linux_x86_64.bin + fetch+http://svn.cgl.ucsf.edu/svn/chimera/trunk/icons/chimera/Chimera512.png" SLOT="0" LICENSE="chimera" KEYWORDS="~amd64 ~x86" -DEPEND="prefix? ( dev-util/patchelf )" +RESTRICT="fetch mirror strip" +QA_PREBUILT="*" + +DEPEND="" +BDEPEND="" RDEPEND=" dev-lang/tcl dev-lang/tk @@ -28,7 +32,6 @@ RDEPEND=" media-libs/libpng media-libs/tiff sci-libs/hdf5 - sci-libs/xdrfile sys-devel/gcc[openmp,fortran] media-libs/libjpeg-turbo virtual/glu @@ -43,32 +46,28 @@ RDEPEND=" x11-libs/libSM x11-libs/libXt x11-libs/libGLw + virtual/libcrypt:= " S="${WORKDIR}" -RESTRICT="fetch mirror strip" - -QA_PREBUILT="opt/.*" - pkg_nofetch() { elog "Please visit" elog "https://www.cgl.ucsf.edu/chimera/download.html" - elog "or" - elog "https://www.cgl.ucsf.edu/chimera/olddownload.html" - elog "and download ${A} into your DISTDIR" + elog "and download chimera-${PV}-linux_x86_64.bin into your DISTDIR" } src_unpack() { - cp "${DISTDIR}"/${A} ${A}.zip - unzip ${A}.zip || die + cp "${DISTDIR}"/chimera-${PV}-linux_x86_64.bin chimera-${PV}-linux_x86_64.bin.zip + unzip chimera-${PV}-linux_x86_64.bin.zip || die } src_install() { chmod +x ./chimera.bin dodir /opt/ ./chimera.bin -d foo || die - doicon foo/chimeraIcon.png + newicon "${DISTDIR}"/Chimera512.png Chimera.png + make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera mv foo "${ED}/opt/${PN}" || die cat >> "${T}"/chimera <<- EOF @@ -82,10 +81,8 @@ src_install() { doexe "${T}"/chimera # point the symlink to the correct location - rm "${ED}/opt/chimera-bin/include/ft2build.h" - dosym ../../../usr/include/freetype2/ft2build.h opt/chimera-bin/include/ft2build.h - - make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon + rm "${ED}/opt/chimera/include/ft2build.h" || die + dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h if use prefix; then local i diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild b/sci-chemistry/chimera/chimera-1.17.3.ebuild index 7d5f9147a..4fdafd361 100644 --- a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild +++ b/sci-chemistry/chimera/chimera-1.17.3.ebuild @@ -1,19 +1,23 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 - +EAPI=8 inherit desktop xdg -DESCRIPTION="An extensible Molecular Modelling System" +DESCRIPTION="Next generation molecular visualization program from RBVI" HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" -SRC_URI="chimera-${PV}-linux_x86_64.bin" +SRC_URI="${P}-linux_x86_64.bin + mirror+https://dev.gentoo.org/~pacho/${PN}/Chimera512.png" SLOT="0" LICENSE="chimera" KEYWORDS="~amd64 ~x86" -DEPEND="prefix? ( dev-util/patchelf )" +RESTRICT="fetch mirror strip" +QA_PREBUILT="*" + +DEPEND="" +BDEPEND="" RDEPEND=" dev-lang/tcl dev-lang/tk @@ -28,7 +32,6 @@ RDEPEND=" media-libs/libpng media-libs/tiff sci-libs/hdf5 - sci-libs/xdrfile sys-devel/gcc[openmp,fortran] media-libs/libjpeg-turbo virtual/glu @@ -43,32 +46,28 @@ RDEPEND=" x11-libs/libSM x11-libs/libXt x11-libs/libGLw + virtual/libcrypt:= " S="${WORKDIR}" -RESTRICT="fetch mirror strip" - -QA_PREBUILT="opt/.*" - pkg_nofetch() { elog "Please visit" elog "https://www.cgl.ucsf.edu/chimera/download.html" - elog "or" - elog "https://www.cgl.ucsf.edu/chimera/olddownload.html" - elog "and download ${A} into your DISTDIR" + elog "and download ${P}-linux_x86_64.bin into your DISTDIR" } src_unpack() { - cp "${DISTDIR}"/${A} ${A}.zip - unzip ${A}.zip || die + cp "${DISTDIR}"/${P}-linux_x86_64.bin ${P}-linux_x86_64.bin.zip + unzip ${P}-linux_x86_64.bin.zip || die } src_install() { chmod +x ./chimera.bin dodir /opt/ ./chimera.bin -d foo || die - doicon foo/chimeraIcon.png + newicon "${DISTDIR}"/Chimera512.png Chimera.png + make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera mv foo "${ED}/opt/${PN}" || die cat >> "${T}"/chimera <<- EOF @@ -82,10 +81,8 @@ src_install() { doexe "${T}"/chimera # point the symlink to the correct location - rm "${ED}/opt/chimera-bin/include/ft2build.h" - dosym ../../../usr/include/freetype2/ft2build.h opt/chimera-bin/include/ft2build.h - - make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon + rm "${ED}/opt/chimera/include/ft2build.h" || die + dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h if use prefix; then local i diff --git a/sci-chemistry/nmrview/metadata.xml b/sci-chemistry/chimera/metadata.xml index 79d42af98..5c83ce208 100644 --- a/sci-chemistry/nmrview/metadata.xml +++ b/sci-chemistry/chimera/metadata.xml @@ -2,8 +2,8 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> + <email>pacho@gentoo.org</email> + <name>Pacho Ramos</name> </maintainer> <maintainer type="project"> <email>sci-chemistry@gentoo.org</email> diff --git a/sci-chemistry/concoord/Manifest b/sci-chemistry/concoord/Manifest index 5607cb51b..053b53267 100644 --- a/sci-chemistry/concoord/Manifest +++ b/sci-chemistry/concoord/Manifest @@ -1,4 +1,2 @@ -DIST concoord2.1_linux_i386.tgz 2948256 BLAKE2B 862de32d37a1680fbc3bdd7512127c2491e421ac63c716dc24ca43e58123ed3f1c00a6d4cb63f91a15d41a3ac0d885c08950de7896abc841167da65a99ce9d80 SHA512 2af10b14f24305dbea4ff12df86ca9bc5e8d2957873756b2f9b5ee57fc7b8db91a787ff09d70ce70a1c3d9278a142474c893250944aa3b8c83862311ed3e3cef -DIST concoord2.1_linux_x86_64.tgz 3352731 BLAKE2B d3ed53866053474378b22bb186822a46c01be4506f09930d26476814591d8c6474d7eff6797c1738c240c1cd8fc840849b9150f30c73aa8f826e246460313251 SHA512 cfb30d7d0950e5978ea0a908a0e607b675333e267ee7da6103ead1b27ceb4dedde42daef3f7027c47e40e01cd247f3e57c5fa13eb76c0f3ac7fa1868f5fb8bf5 DIST concoord_2.1.2_linux32.tgz 1193266 BLAKE2B 2adb51fdba074d608a2dc172556d5a0f37df2d8b7259b36da7d4330ded4a81f104b2c0ba1f18505141204d507f60b9bbfeffbc91eb2d129918fec9ad28ddde6c SHA512 d74f2fdbb6184f79d3c0770cfa01324dd52448f3a865f5fb379a51431024b843537b8de551aacd2b0117736f7cb2412379cf23e765716969c1ab3069e6e75ea2 DIST concoord_2.1.2_linux64.tgz 1431558 BLAKE2B 6e8d8d42bd629a79e86e84874590a66dc8b30269bda18fb75b91e3dcb84b4e8c36d61177e10282b0421f68d3828cd407f0d81f976f8aa32f28bd9dfb34506fd1 SHA512 e625e10ebe2e5ef6a84af3fe665e792d59ffed3df009f19d66ec0972bd88ec91167e3ec0eee9a72b1c35ba0a85ec70fa5420a7718b83e238b167ad31d95303cf diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild deleted file mode 100644 index 2926f76c8..000000000 --- a/sci-chemistry/concoord/concoord-2.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Protein conformations around a known structure based on geometric restrictions" -HOMEPAGE="https://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html" -SRC_URI=" - amd64? ( https://www3.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_x86_64.tgz ) - x86? ( https://www3.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_i386.tgz )" - -SLOT="0" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="all-rights-reserved" - -QA_PREBUILT="opt/${PN}/bin/*" - -S="${WORKDIR}"/${PN}${PV} - -src_install() { - insinto /opt/${PN}/ - rm lib/*.a || die - doins -r lib - exeinto /opt/${PN}/bin - doexe bin/* - cat >> "${T}"/60${PN} <<- EOF - CONCOORDLIB="${EPREFIX}/opt/${PN}/lib" - CONCOORDBIN="${EPREFIX}/opt/${PN}/bin" - PATH="${EPREFIX}/opt/${PN}/bin" - EOF - doenvd "${T}"/60${PN} -} diff --git a/sci-chemistry/ctffind/Manifest b/sci-chemistry/ctffind/Manifest index 96d9b2769..103ece6da 100644 --- a/sci-chemistry/ctffind/Manifest +++ b/sci-chemistry/ctffind/Manifest @@ -1 +1,3 @@ +DIST ctffind-4.1.10.tar.gz 625495 BLAKE2B 29c16308005322f53de8e0e9e9c03bc4219f5499bdd303d08e6ee93debe022151fc6b4ea5a2dec3f5c155e26913ae678de98a9b8b37f10d391c284011399f36a SHA512 abaa94781a16b6a72d5ed461f89c1aa313540e4d982c75e81879df2e863bf3ff8ad9fb30d00df603bdc7b56565508e9caba31ef2af67a4a8b732df33b53ee4c6 +DIST ctffind-4.1.13.tar.gz 637267 BLAKE2B 89440d497c6cfe962fd6af14ebc78049ff7341f246bb794384337d7b69571e9123da2bb200f34bf6fdafd984e7f38a77ed1f11a2a4da30f1463b6cfdded0d247 SHA512 1523856b75431b1cdbc3d29336f7d59bf0e7ecee70573c79273a97661e75387aa78c91c3d337431a432e1b15760ca34ad2692832f2f57bdc37951d1bc03958eb DIST ctffind-4.1.14.tar.gz 662195 BLAKE2B cb81a971c74e8f2b38e87945aca9f34d4d9cf90770b149ddc5febaee9af4a7392e1d295b2146a14212ea7c820ebf51c5179811cd42875b8a0ef279f6a07e8642 SHA512 115d04ad1adce3f8a99b14e15844df8d6caa4b873faa24eed9d6999a48e88f5a35ffd0cffa6c50c38566cc0091e0de5baec4d0cc62719540a9cfe67bc7333d42 diff --git a/sci-chemistry/ctffind/ctffind-4.1.10.ebuild b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild new file mode 100644 index 000000000..a69a36308 --- /dev/null +++ b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild @@ -0,0 +1,37 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +WX_GTK_VER="3.0-gtk3" +inherit wxwidgets + +DESCRIPTION="CTF estimation (ctffind, ctftilt)" +HOMEPAGE="https://grigoriefflab.umassmed.edu/" +SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz" + +LICENSE="Janelia-1.2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + sci-libs/fftw:3.0 + media-libs/libjpeg-turbo + media-libs/tiff + x11-libs/wxGTK:* +" +RDEPEND="${DEPEND}" +BDEPEND=" + ${DEPEND} + virtual/pkgconfig" + +src_prepare() { + default + sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed" + sed /water/d -i src/core/core_headers.h || die "removing water.h failed" +} + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-chemistry/ctffind/ctffind-4.1.13.ebuild b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild new file mode 100644 index 000000000..a69a36308 --- /dev/null +++ b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild @@ -0,0 +1,37 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +WX_GTK_VER="3.0-gtk3" +inherit wxwidgets + +DESCRIPTION="CTF estimation (ctffind, ctftilt)" +HOMEPAGE="https://grigoriefflab.umassmed.edu/" +SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz" + +LICENSE="Janelia-1.2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + sci-libs/fftw:3.0 + media-libs/libjpeg-turbo + media-libs/tiff + x11-libs/wxGTK:* +" +RDEPEND="${DEPEND}" +BDEPEND=" + ${DEPEND} + virtual/pkgconfig" + +src_prepare() { + default + sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed" + sed /water/d -i src/core/core_headers.h || die "removing water.h failed" +} + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml index eea62e858..996e48735 100644 --- a/sci-chemistry/erkale/metadata.xml +++ b/sci-chemistry/erkale/metadata.xml @@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules. </longdescription> + <upstream> + <remote-id type="github">susilehtola/erkale</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild deleted file mode 100644 index e42a795f1..000000000 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake fortran-2 git-r3 python-any-r1 - -DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" -HOMEPAGE="https://www.freeon.org" -EGIT_REPO_URI="https://github.com/FreeON/freeon.git" -EGIT_BRANCH="master" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -RDEPEND=" - sci-libs/hdf5 - virtual/blas - virtual/lapack -" -DEPEND="${RDEPEND} - ${PYTHON_DEPS}" diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml deleted file mode 100644 index 2fe5325ae..000000000 --- a/sci-chemistry/freeon/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>nicolasbock@gentoo.org</email> - <name>Nicolas Bock</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild index 17fe76f76..173e3513e 100644 --- a/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild +++ b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild @@ -272,7 +272,7 @@ src_compile() { ./compall || die "compall failed" # build the ddi TCP/IP socket stuff - cd ${S}/"ddi" + cd "${S}/ddi" ./compddi || die "compddi failed" # finally, link it all together diff --git a/sci-chemistry/ligplot+/Manifest b/sci-chemistry/ligplot+/Manifest deleted file mode 100644 index 996b438bb..000000000 --- a/sci-chemistry/ligplot+/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST LigPlus.zip 1937904 SHA256 5d47af05f1fb48b4c0a6dee4d8eacb0d2ffe90966b0419d954c9d0f7a6580b49 SHA512 fee1c9b54c895d26ebd81f283ab942b199db87d189a01f22aebf26d6ed90e801f53b64cf9abf870721a4b478e68bf390b0e1c9eb9b02a692a1011271611f7afd WHIRLPOOL d86822b5e4cd0bd429df912f3b60de11094a2e549841f59343c0435a329a5c1181e543e06af9eb760d3bbbc6a12414fc5477c87f192deb40304d7ce619b65f28 diff --git a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild deleted file mode 100644 index 80963ed83..000000000 --- a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 wrapper - -DESCRIPTION="GUI-based version of LIGPLOT" -HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/LigPlus/" -SRC_URI="LigPlus.zip" - -SLOT="0" -LICENSE="ligplot+" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="virtual/jre:*" -DEPEND="app-arch/unzip" - -RESTRICT="fetch" - -S="${WORKDIR}/LigPlus" - -QA_PREBUILT="opt/${PN}/.*" - -pkg_nofetch() { - elog "Please visit" - elog "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html" - elog "download ${A}" - elog "and save into your DISTDIR folder" -} - -src_prepare() { - default - rm -rf lib/*{win,mac} || die -} - -src_install() { - insinto /opt/${PN} - doins -r lib LigPlus.jar - - make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\"" -} diff --git a/sci-chemistry/ligplot+/metadata.xml b/sci-chemistry/ligplot+/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/ligplot+/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/mage/Manifest b/sci-chemistry/mage/Manifest deleted file mode 100644 index 72cb530fd..000000000 --- a/sci-chemistry/mage/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mage.6.44.060606.src.tgz 726357 BLAKE2B e427bf0707b192653c6cafd392a6ceaf49ec45fcff5447c42b4dd7e0e75ff46bf78edd9b03260cfe0d465c6ae0c6b1ff6a6340fb4fdf34feec1dba13a971d3ca SHA512 dceb63cc9806690539d0838079c2b57d6e62164049ca178d158e9c7eae759988c28d7e911942fd50f1ea880e61b2e9d7a38cc64bc5c229a4e5d442357c1f9227 diff --git a/sci-chemistry/mage/files/6.44.060606-Makefile.patch b/sci-chemistry/mage/files/6.44.060606-Makefile.patch deleted file mode 100644 index df4fa4e1a..000000000 --- a/sci-chemistry/mage/files/6.44.060606-Makefile.patch +++ /dev/null @@ -1,29 +0,0 @@ -diff --git a/Makefile b/Makefile -index 62a2033..1722ba5 100644 ---- a/Makefile -+++ b/Makefile -@@ -11,7 +11,7 @@ - # and static compile fails for RH 7.2 and 7.3 - # - ifeq ($(MAKECMDGOALS),dynamic) --CFLAGS = -I/usr/X11R6/include #for RH7.3 -+CFLAGS += -I/usr/X11R6/include #for RH7.3 - # CFLAGS = -I/usr/X11R6/LessTif/Motif1.2/include/ #for RH7.1 - else #for RH8.0 - CFLAGS = -D_STATIC_ -@@ -80,13 +80,13 @@ static: $(OBJS) dlstubs.o - $(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN) - - dynamic: $(OBJS) -- $(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) - # $(CC) -o mage $(OBJS) -L/usr/X11R6/LessTif/Motif1.2/lib $(LIBS) -ldl $(FIN) - # where RH7.1 needed explicit LessTif and could compile static - # RH7.3 fails static in all tried cases, but has Xm libraries implicit - - debug: $(OBJS) -- $(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) - - debugs: $(OBJS) dlstubs.o - $(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN) diff --git a/sci-chemistry/mage/files/digest-mage-6.44.060606 b/sci-chemistry/mage/files/digest-mage-6.44.060606 deleted file mode 100644 index a73fa1c02..000000000 --- a/sci-chemistry/mage/files/digest-mage-6.44.060606 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 aa49ae2cd466d718891391f593202f97 mage.6.44.060606.src.tgz 726357 -RMD160 08305d65dd61ed573c67e58975a611439235e9f5 mage.6.44.060606.src.tgz 726357 -SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 mage.6.44.060606.src.tgz 726357 diff --git a/sci-chemistry/mage/mage-6.44.060606.ebuild b/sci-chemistry/mage/mage-6.44.060606.ebuild deleted file mode 100644 index bffe9c21f..000000000 --- a/sci-chemistry/mage/mage-6.44.060606.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="${PN}.${PV}" - -DESCRIPTION="Mage is a 3D vector display program which shows 'kinemage' graphics" -HOMEPAGE="http://kinemage.biochem.duke.edu/software/mage.php" -SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/mage/${MY_P}.src.tgz" - -LICENSE="richardson" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="sci-chemistry/prekin" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}/${PV}-Makefile.patch" -) - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - dynamic -} - -src_install() { - dobin "${S}"/mage -} diff --git a/sci-chemistry/mage/metadata.xml b/sci-chemistry/mage/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/mage/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?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/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest index 2da2b203c..c54650082 100644 --- a/sci-chemistry/nmrpipe/Manifest +++ b/sci-chemistry/nmrpipe/Manifest @@ -1,6 +1,6 @@ -DIST NMRPipeX-8.7.20200827.tZ 65154741 BLAKE2B c4eafa6496476046acf44e99063d18fed1e77bca1af749c92305f6c9b0ed5ec045f8fe611c34324eb03b1631be0bc68eb6fbf915fd2fdd02dfd41b6cfd6027b2 SHA512 0b84d655aa8b76e3b877e229e1f256403d1d714b7178bc39c4e213a238dc5614ff36fca8e36b285668eb0135134c975a108f447021c3442e9864554aadee8d00 -DIST binval-8.7.20200827.com 3745 BLAKE2B 18b99fb2286a94ce2d0c8d8792e4384c8042b7ce7c43a0aee189af3185db181fc9fc829d186684423f8360a2b681bfcf18d419f05c58352b32967117252465d7 SHA512 f857126b65d27436e471e8e45be049ef892a80272a7f0da97db81d6861f18024ced527da24ab0fdc8ef91c0ec66211ad72703d7ccdcd133babbc51eacfced9ba -DIST dyn-8.7.20200827.tZ 301148865 BLAKE2B 9706a163bdd2947e909a79333a4a50b58e09e7daa11d958dde805681e92ecff17204bd896bd4b1658a10fc2113ae4339e7f54636ebbb17d00845b95846023cd8 SHA512 2dd7dbbc6e4c0bceedfe7923e89095e6755e5f92b3a7635e70ef6a51570e88c4edf98387ccfd353b8450b46fe0aa6a56f3fe778a9492e85abfb0e4b15cdca1aa -DIST install-8.7.20200827.com 50940 BLAKE2B cc1e492549e3ab4377f607ab4e59ab1b344ece3ab0332cddc43c71b827e3224d77d4dec6101766e9f885db669f56a011fec8dbb2d512eb7e7c1ae665a1f6c829 SHA512 fdb8bcfa0f4ecac3f6690322db163695446b58a536411a503c80fe222b9995c395f0ba5e6b8933d7c1a8a4dca984ad2aa5c12aa8eef2fd985c7b18da431f5126 -DIST plugin.smile-8.7.20200827.tZ 77264061 BLAKE2B 04b464a00b2cf26ed309b4cb89b37f23dde38ffeedc848167fd1beeeed699c576fecf9fa3ba4bcfe5f597113c19d06e0bfd6210d24efdda9ee8b41d908295db3 SHA512 92c172fedf00fe31d68a532d9d40a63bd0e284b153a4b54d2b0d21a820ceba3b52e13e278c6f40a734e367e6f7b6b27bd470efcf6ef328c9017fad60a77361ac -DIST talos-8.7.20200827.tZ 209214741 BLAKE2B 63d84972c556d1fb5c5f5b4ab9b56e7eb5c48a9487d846dd09a3d6713a9228417431f40e965c4781c66b8c80655a2248eafec1b48163cc132e031382429f7092 SHA512 61d8cf81ae8dd316a7c68c1110ee4b12b36c0319ee89fbc4b0a2e67559527a57204ff270f008c25f000f17f0d893c6342d84af36b2af59088cfb255385899dcb +DIST NMRPipeX-8.7.20230206.tZ 100114853 BLAKE2B 6e0dda8ef3946ea2397f2a394529a2c20b09f4f6dc7f56205b17c35d0a0d09519f92899f0628070cf5f24aec41d71b54fc606f7d6a01f0ccb79f69fe59234b56 SHA512 0ec09385f0181af58a5ad1ba5335e32e1544d73b1322b2764b738474cbb96128158b6739684e0e008411c27bed831d58fd44953494c790bf20796cf82750792e +DIST binval-8.7.20230206.com 4004 BLAKE2B cf8d84c533431b6eeaa031285071abdd241a5774c4731a650084e312c2e3094c2a26e54432e8e9abb42280f2968dee276918659ba9e036587e799618d5dfb829 SHA512 ef47c209848a479e0c6f7f9a472279e6260cb56311e9571da22b474e520515abc64e75cc5dd7817bb629497e0a83c53a6f847904e08004e0b2d09ba035f688a9 +DIST dyn-8.7.20230206.tZ 301148865 BLAKE2B 11cdebd68efa2ed758309f27ba8fd57b6e659d9cdf98d3708c85f65b181eca42dc6fae832db13e9684e4f710d8f0ec7d60d7cc4d5dc698f730dcce317df0d56a SHA512 e5dc12af048f8f87c13c60c020df5ae47afaaa869852134563124bcc2f344176f1da452ce92169ed3cf2c7c4e505d6498bd60fb5ba1b3de489a9791e25f0354c +DIST install-8.7.20230206.com 50938 BLAKE2B ad8039df53d5069ed5b74be3d085fb0b11fda0a3b585d7992ed3634f383bb8b21c31c808befb9e917882392a0333da898a97d423c61cad49ac351f12fd8c4df4 SHA512 0b1aea3ab316dd29108cce60a4d1aa84835ab088389d6e46d8ee3c7bffb75d38506bac35f5e0c202dc9bf040e2e8418697126a3aa8dc6f256e3c75614b52a30c +DIST plugin.smile-8.7.20230206.tZ 73190777 BLAKE2B 94471d441a82a35feb9ce7c7fca52e343ea5ad4d8688dce09e23c9f6a76288de3a080cb587e4b44800d0c1401aebc0586753a83b4b6370030221519b2f34ba13 SHA512 511c39bbf3d9bd608cfb53a8720f26a1e201d3065e0109f8a11ee513ff0f160f3866099f88d359ec301cdfde05ef84b43a694846494bd4231bf4b401dd33e6b3 +DIST talos-8.7.20230206.tZ 209640635 BLAKE2B bb5fc9a925dbc5e553711a63177c69e8c01d4cdfacf4ec04960fe21d4996aeee35287686d89452dfc51f94712c1c42e9ab316073072f92f9576418ec282f9988 SHA512 3225f40dd4437e18d3dc8d3c1874df10b7257ee6f556cef8d2e77e90d64308799499aa70020b6c2b7152121c1124fac744e553b770097b544a9b888505250711 diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.7.20200827.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild index 303f2c4a2..650c35305 100644 --- a/sci-chemistry/nmrpipe/nmrpipe-8.7.20200827.ebuild +++ b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild @@ -3,7 +3,7 @@ # Versioning is output of nmrPipe -help -EAPI=7 +EAPI=8 inherit virtualx diff --git a/sci-chemistry/nmrview/Manifest b/sci-chemistry/nmrview/Manifest deleted file mode 100644 index c5cae1ddf..000000000 --- a/sci-chemistry/nmrview/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST nmrview5.2.2.lib.tar.gz 4097039 SHA256 96965ab68566b4d4b3873d53e0cf88f0bb5757d9d30dcabbbcb7e062008aac4e SHA512 6d5675a329371a63f16a0119cb71fcc8377a4a827c3d9e5eb3fc1dcef671ad28adc95ac19b99ffcc8431af5057715beda90c7d2853b65fe6c5aa40a272db6b16 WHIRLPOOL 8759f05384187c4146e7c7591fac72729c3ec808bed451c5fd53400e557b073250856e65ddb04fdf65f960af0d0a461afd9a8afcb542c28be9e78dc12a6e5cd2 -DIST nmrview5_2_2_01_linux.gz 963243 SHA256 ac60d882c6c1c9179f612e37e4257dbab819b5b4fbc215189441124815525b55 SHA512 99745586cde0927cb0942d3c5c2f4b9ef9d52f0c650325971526b9fa4d14bdd5fad89561805526f62e667d6ad9bc18e0929eb0a5d75a17e040bd3142d88c37cf WHIRLPOOL 1851ab48029443e294a4cb2b961c4b9bde1ef19e15e70208a163b374da3964e1573184856d9010c4181a7649d471333d71370db6326cba5429c1cee4e1c8f330 diff --git a/sci-chemistry/nmrview/files/README.Gentoo b/sci-chemistry/nmrview/files/README.Gentoo deleted file mode 100644 index fbb0fdf2f..000000000 --- a/sci-chemistry/nmrview/files/README.Gentoo +++ /dev/null @@ -1,17 +0,0 @@ -Using NMRView on Gentoo - -NMRView may be launched via the "nmrview "wrapper script installed in -"/usr/bin". The script will pass on all positional parameters to the NMRView -binary, so you may specify a start up script or a database to open on the -command line. - -If you want a convenient way to set up multiple configurations, you can use -shell aliases to redefine the "nmrview" command or to add new commands starting -nmrview with different startup scripts, databases, etc. The following example -alias declarations (for bash) could be put in "~/.bashrc" to redefine the -"nmrview" command to launch NMRView with a default startup file, and to add a -new command to launch the program with an alternative startup file and -application name. - -alias nmrview="nmrview -- -s ${HOME}/.nmrview/startup" -alias nmrview-dyn="nmrview -name nmrview-dyn -- -s ${HOME}/.nmrview/startup-dyn" diff --git a/sci-chemistry/nmrview/files/nmrview.sh b/sci-chemistry/nmrview/files/nmrview.sh deleted file mode 100644 index d879865e8..000000000 --- a/sci-chemistry/nmrview/files/nmrview.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -export NMRVIEW5HOME="/opt/nmrview" -export TK_LIBRARY="/opt/nmrview/tk8.4" -export TCL_LIBRARY="/opt/nmrview/tcl8.4" -/opt/nmrview/nmrview5_2_2_01_linux diff --git a/sci-chemistry/nmrview/files/nmrview.sh-r1 b/sci-chemistry/nmrview/files/nmrview.sh-r1 deleted file mode 100644 index 9e122d0c5..000000000 --- a/sci-chemistry/nmrview/files/nmrview.sh-r1 +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -export NMRVIEW5HOME="/opt/nmrview" -export TK_LIBRARY="/opt/nmrview/tk8.4" -export TCL_LIBRARY="/opt/nmrview/tcl8.4" -/opt/nmrview/nmrview5_2_2_01_linux $@ diff --git a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild deleted file mode 100644 index 231d237bc..000000000 --- a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Visualisation and analysis of processed NMR data" -HOMEPAGE="https://nmrfx.org/nmrfx/nmrviewj" -SRC_URI=" - ${PN}${PV}.lib.tar.gz - ${PN}${PV//./_}_01_linux.gz" - -SLOT="0" -LICENSE="all-rights-reserved" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="x11-libs/libX11" -DEPEND="" - -RESTRICT="fetch" - -S="${WORKDIR}" - -INSTDIR="/opt/nmrview" - -QA_PREBUILT="/opt/nmrview/nmrview5_2_2_01_linux" - -pkg_nofetch() { - einfo "Please visit:" - einfo "\t${HOMEPAGE}" - echo - einfo "Complete the registration process, then download the following files:" - einfo "\t${A}" - echo - einfo "Place the downloaded files in your distfiles directory" - echo -} - -src_install() { - insinto ${INSTDIR} - - sed \ - -e "s:/opt:${EPREFIX}/opt:g" \ - "${FILESDIR}"/${PN}.sh-r1 \ - > "${T}"/${PN} || die - - dobin "${T}"/${PN} - exeinto ${INSTDIR} - doexe ${PN}${PV//./_}_01_linux - - DIRS="help html images nvtcl nvtclC nvtclExt reslib star tcl8.4 tk8.4 tools" - doins -r ${DIRS} - - dodoc "${FILESDIR}"/README.Gentoo - doins README - dosym ${INSTDIR}/html /usr/share/doc/${PF}/html - dosym ${INSTDIR}/README /usr/share/doc/${PF}/README -} diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest deleted file mode 100644 index 976149b88..000000000 --- a/sci-chemistry/pymol-plugins-psico/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-psico-3.4.tar.gz 88984 BLAKE2B 9ea006add8f24d41a8d9523fcb1bc6f5b9b98a93284da6db24e2faef69d713ed671d38aa2e424c4cf0400fbfb0b14ff06c0974f9abfdf9ffd5aa8db3dd311788 SHA512 846ae385751760c4760d044b71bbb6925abd0e91978390e7f2fa03618145ff9feef88df569b5bc7fd1398fdd44cdabe416efc21b46fee7b294283082096a1282 diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml deleted file mode 100644 index 9d384241e..000000000 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>jlec@gentoo.org</email> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="github">speleo3/pymol-psico</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild deleted file mode 100644 index 471e85be8..000000000 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=no - -inherit distutils-r1 optfeature - -DESCRIPTION="Pymol ScrIpt COllection" -HOMEPAGE="https://github.com/speleo3/pymol-psico/" -SRC_URI="https://github.com/speleo3/pymol-psico/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="BSD-2" - -S="${WORKDIR}/pymol-psico-${PV}" - -RDEPEND=" - sci-chemistry/pymol[${PYTHON_USEDEP}] -" - -pkg_post_inst() { - optfeature sci-libs/mmtk "Normal modes via mmtk" -} diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest index 6aa383614..75b932e28 100644 --- a/sci-chemistry/relion/Manifest +++ b/sci-chemistry/relion/Manifest @@ -1 +1,2 @@ -DIST relion-3.1.1.tar.gz 2340685 BLAKE2B 0e98db3af7ceb312111260d8af51225d9a6b82314f1f066fe52464b533e59f44f5487ba66110708d661506074be4d52eeb7e04d88344a939bbd33139a33f6dec SHA512 fddf6f8a3d63e4f73aa1f529e4fa8fa7da98d9226b6539530c83496b94793ceef27d013a2d902a794993ab994f8d6467569ea4b681b4dd948654acf482529b22 +DIST class_ranker_0.1.3_torch_1.0.1.pt.tar.gz 2190018 BLAKE2B 157d380693cb97f2f94aea5ee8b1c9b64c50cead45c65d8d95584b12a4901622df025e4bdfccfc9c87286a3d442ffc26ed2a89953b9361f59d7ae2852fcc3a6b SHA512 0e9d4046a9ba211c07abcc44d0b51c7d69805eb946ed96abdd1663760906188050d476268214b4e7a84f529f51226c39f40c3b418373437fae2f4bb24990f338 +DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209 diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch new file mode 100644 index 000000000..d7cb7bf2e --- /dev/null +++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch @@ -0,0 +1,39 @@ +From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001 +From: Takanori Nakane <nakane.t@gmail.com> +Date: Fri, 28 Oct 2022 19:51:29 +0900 +Subject: [PATCH] Repaired the build failure reported in #826 (by + @prehensilecode and @acaprez) + +--- + src/apps/CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt +index 9870b735..30985aa7 100644 +--- a/src/apps/CMakeLists.txt ++++ b/src/apps/CMakeLists.txt +@@ -273,16 +273,16 @@ if (CUDA_FOUND) + + + +- file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" ) ++ file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu") + cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC}) + +- #list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") +- #if(BUILD_SHARED_LIBS) +- # install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) +- #else() +- # target_link_libraries(relion_jaz_gpu_util relion_lib) +- # target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) +- #endif() ++ list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") ++ if(BUILD_SHARED_LIBS) ++ install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) ++ else() ++ target_link_libraries(relion_jaz_gpu_util relion_lib) ++ target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) ++ endif() + + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY}) diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml index cdabe7f2c..101a056b9 100644 --- a/sci-chemistry/relion/metadata.xml +++ b/sci-chemistry/relion/metadata.xml @@ -11,5 +11,9 @@ </maintainer> <use> <flag name="gui">Enable relion gui</flag> + <flag name="cuda">Enable CUDA support</flag> </use> + <upstream> + <remote-id type="github">3dem/relion</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-3.1.1.ebuild deleted file mode 100644 index 39e4ab229..000000000 --- a/sci-chemistry/relion/relion-3.1.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Image-processing software for cryo-electron microscopy" -HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" -SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+gui" - -DEPEND=" - gui? ( x11-libs/fltk ) - dev-cpp/tbb - sci-libs/fftw:3.0 - media-libs/tiff - virtual/mpi -" -RDEPEND=" - ${DEPEND} - sci-chemistry/ctffind -" -BDEPEND="${DEPEND}" - -src_configure() { - CMAKE_BUILD_TYPE=Release - mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DALTCPU=$(usex !cuda) - -DFORCE_OWN_FFTW=OFF - -DFORCE_OWN_FLTK=OFF - -DFORCE_OWN_TBB=OFF - -DCUDA=OFF - -DGUI=$(usex gui) - ) - cmake_src_configure -} diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild new file mode 100644 index 000000000..c6d7d90db --- /dev/null +++ b/sci-chemistry/relion/relion-4.0.0.ebuild @@ -0,0 +1,71 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" ) + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} diff --git a/sci-chemistry/relion/relion-9999.ebuild b/sci-chemistry/relion/relion-9999.ebuild new file mode 100644 index 000000000..12e09d2fe --- /dev/null +++ b/sci-chemistry/relion/relion-9999.ebuild @@ -0,0 +1,69 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} diff --git a/sci-chemistry/rosetta-tools/Manifest b/sci-chemistry/rosetta-tools/Manifest deleted file mode 100644 index 912e8c895..000000000 --- a/sci-chemistry/rosetta-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST BioTools-3.0.tgz 41121 SHA256 363689571fd131ba0e9b4fdbe239868c3a78b7104270f5b2d0285b0f96af4f9c diff --git a/sci-chemistry/rosetta-tools/metadata.xml b/sci-chemistry/rosetta-tools/metadata.xml deleted file mode 100644 index a5629e344..000000000 --- a/sci-chemistry/rosetta-tools/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?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> - <upstream> - <remote-id type="sourceforge">dylans-biotools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild b/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild deleted file mode 100644 index bbe5b2b8d..000000000 --- a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -MY_PN="BioTools" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Additional scripts for rosetta" -HOMEPAGE="http://www.rosettacommons.org/ http://dylans-biotools.sourceforge.net/" -SRC_URI="${MY_P}.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="dev-lang/perl" - -RESTRICT="fetch" - -S="${WORKDIR}/${MY_PN}" - -src_install() { - local x - for x in $(ls *.pl); do - newbin ${x} ${x%.pl} - done -} |