diff options
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/Manifest.gz | bin | 17228 -> 17230 bytes | |||
-rw-r--r-- | sci-chemistry/molmol/Manifest | 6 | ||||
-rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r2.ebuild | 80 | ||||
-rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r3.ebuild | 84 | ||||
-rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r4.ebuild | 86 | ||||
-rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r5.ebuild | 51 | ||||
-rw-r--r-- | sci-chemistry/pymol/Manifest | 4 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-2.2.0.ebuild | 114 | ||||
-rw-r--r-- | sci-chemistry/pymol/pymol-2.3.0-r1.ebuild (renamed from sci-chemistry/pymol/pymol-2.3.0.ebuild) | 7 | ||||
-rw-r--r-- | sci-chemistry/vmd/Manifest | 4 | ||||
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 8 | ||||
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 | ||||
-rw-r--r-- | sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 262 |
13 files changed, 321 insertions, 398 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 88dc6c45c203..556564f17fc7 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index 3fb7f463629c..d8afb6a89cc3 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -1,8 +1,6 @@ DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 -EBUILD molmol-2k_p2-r2.ebuild 1786 BLAKE2B eda77c9e82f6b48eb38c5f47dfdd74d5916f376cc2d07fe54542fef4c1c7ecffd90ec3af82f4abd8453b15ea2044f56280dfa14274aa3d8a549136153f43c709 SHA512 cffa98ccf69382a64b4005d8971e6ecd1ed02d4199d8b494819d62439daa74b50244f6cb599c7ea73231d60f2d45d1aa49543121fc07b0e7d2ae30da044b7240 -EBUILD molmol-2k_p2-r3.ebuild 1918 BLAKE2B 134be8d8f1c11b60117c701a9b19c5f857dc554d8cd3221eae63d8f8f2d1e7d6382da8071c1d10f08294823bb1e8acabe7c3018d4817ecc9e62959f1fb204c22 SHA512 a1442eb74cc7aaa49ca81765601d1272138ed2ca3d7cebdadedd3bee4f561abf340bcfeabe4556d893df8d1be7983ac488b8773661ffc74a93a379fd503ebf0d -EBUILD molmol-2k_p2-r4.ebuild 1935 BLAKE2B f0efe15c919180becacbd408e9974b7699276c31307773865c78ba4a2c2d122dee693af69d3aac14f3f58417410cfc0c0701207870bd474e0cda546dceab24d9 SHA512 3a59f7e5df34e0762289e6156a24bbaa7f1853c54c8db3436beae457f1c4f7e49656234f843d529099d9e2ad79ade7aff6f463f12fd5495c58265f538156c180 -EBUILD molmol-2k_p2-r5.ebuild 1947 BLAKE2B 85d1f2c7dde895f466fa334f5163be3b21eca7cc06cadb1fa15598351ea5f4bc0400680f92ed69e42031e3bfbe6a7ffcb85d9460e55055d3760eed5429360038 SHA512 6c0b9db7453acb3a14d762317548ace5a88143d9d3add2104acab0c7c2a7c6901b2086edf5bd5c48caa5fa1059664cf2c24304a88ba28e26ff77f895c1f03084 +DIST molmol.png 509 BLAKE2B 981217602d128da2eb3765ca07580ed58164a4aa8c2d3e016cd54d9f5133418a7c87bbf0f8a83bcbd5d60ad568bf4938ce680eea315716166592e37f815b5aab SHA512 233d3be0c2e2759a8b064b4cf3708f96817f34eb2a397d5122b26a902864a0f1dca1762f8bcc6981cd030e2644cbedef9eb20c7756016fcf27565e3ed586c271 +EBUILD molmol-2k_p2-r5.ebuild 2222 BLAKE2B 701c748446929618b42916e94b2742969d7b66acb055dab37834463bd5420f22e2d0119440dd58685236054a61745a36d8cd385dfd1593217595a48f9978111b SHA512 49dafa2d8a771ec2f8e3ff76f16790d61de84419037f7132581ef5de3f7c2ba12aedaf2ec778139420996d610788aef4c23ee8ac4339a8fe81cba4d36f99ebf8 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild deleted file mode 100644 index 888c738d4f15..000000000000 --- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils multilib prefix toolchain-funcs - -MY_PV="${PV/_p/.}.0" -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="Publication-quality molecular visualization package" -HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" -SRC_URI=" - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" - -LICENSE="molmol" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - || ( - ( media-libs/mesa - x11-libs/libGLw ) - media-libs/mesa[motif] ) - media-libs/libpng:0 - media-libs/tiff:0 - sys-libs/zlib - virtual/glu - virtual/jpeg - x11-libs/libXpm - x11-libs/motif:0 - x11-apps/xdpyinfo" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -MAKEOPTS="${MAKEOPTS} -j1" - -pkg_setup() { - MMDIR="/usr/$(get_libdir)/molmol" -} - -src_prepare() { - rm -rf tiff* - # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - - epatch "${WORKDIR}"/patches/prefix.patch - eprefixify molmol - - epatch "${WORKDIR}"/patches/ldflags.patch - - ln -s makedef.lnx "${S}"/makedef || die - - sed \ - -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ - -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ - -i "${S}"/molmol || die - sed \ - -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -i "${S}"/makedef || die - - epatch "${WORKDIR}"/patches/cast.patch - epatch "${WORKDIR}"/patches/libpng15.patch -} - -src_install() { - dobin molmol - - exeinto ${MMDIR} - newexe src/main/molmol molmol.lnx - insinto ${MMDIR} - doins -r auxil help macros man setup tips - - dodoc HISTORY README -} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild deleted file mode 100644 index 22f3e6a03bdf..000000000000 --- a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=4 - -inherit eutils multilib prefix toolchain-funcs - -MY_PV="${PV/_p/.}.0" -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="Publication-quality molecular visualization package" -HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" -SRC_URI=" - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" - -LICENSE="molmol" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - || ( - ( media-libs/mesa - x11-libs/libGLw ) - media-libs/mesa[motif] ) - media-libs/libpng:0 - media-libs/tiff:0 - sys-libs/zlib - virtual/glu - virtual/jpeg - x11-libs/libXpm - x11-libs/motif:0 - x11-apps/xdpyinfo" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -MAKEOPTS="${MAKEOPTS} -j1" - -pkg_setup() { - MMDIR="/usr/$(get_libdir)/molmol" -} - -src_prepare() { - rm -rf tiff* - # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - - epatch "${WORKDIR}"/patches/prefix.patch - eprefixify molmol - - epatch "${WORKDIR}"/patches/ldflags.patch - - ln -s makedef.lnx "${S}"/makedef || die - - sed \ - -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ - -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ - -i "${S}"/molmol || die - sed \ - -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -i "${S}"/makedef || die - - epatch "${WORKDIR}"/patches/cast.patch - epatch "${WORKDIR}"/patches/libpng15.patch - - # patch from fink - # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${WORKDIR}"/patches/${P}-fink.patch -} - -src_install() { - dobin molmol - - exeinto ${MMDIR} - newexe src/main/molmol molmol.lnx - insinto ${MMDIR} - doins -r auxil help macros man setup tips - - dodoc HISTORY README -} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild deleted file mode 100644 index 26a294922182..000000000000 --- a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild +++ /dev/null @@ -1,86 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils multilib prefix toolchain-funcs - -MY_PV="${PV/_p/.}.0" -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="Publication-quality molecular visualization package" -HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" -SRC_URI=" - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" - -LICENSE="molmol" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - || ( - ( media-libs/mesa - x11-libs/libGLw ) - media-libs/mesa[motif] ) - media-libs/libpng:0 - media-libs/tiff:0 - sys-libs/zlib - virtual/glu - virtual/jpeg:0 - x11-libs/libXpm - x11-libs/motif:0 - x11-apps/xdpyinfo" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -MAKEOPTS="${MAKEOPTS} -j1" - -pkg_setup() { - MMDIR="/usr/$(get_libdir)/molmol" -} - -src_prepare() { - rm -rf tiff* - # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - - epatch "${WORKDIR}"/patches/prefix.patch - eprefixify molmol - - epatch "${WORKDIR}"/patches/ldflags.patch - - ln -s makedef.lnx "${S}"/makedef || die - - sed \ - -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ - -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ - -i "${S}"/molmol || die - sed \ - -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ - -e "s:^CC.*:CC = $(tc-getCC):" \ - -i "${S}"/makedef || die - - epatch "${WORKDIR}"/patches/cast.patch - epatch "${WORKDIR}"/patches/libpng15.patch - - # patch from fink - # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${WORKDIR}"/patches/${P}-fink.patch - - tc-export AR -} - -src_install() { - dobin molmol - - exeinto ${MMDIR} - newexe src/main/molmol molmol.lnx - insinto ${MMDIR} - doins -r auxil help macros man setup tips - - dodoc HISTORY README -} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild index 41b041609f2f..a09bfe07847b 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild @@ -1,39 +1,48 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 - -inherit eutils multilib prefix toolchain-funcs +EAPI=7 +inherit desktop prefix toolchain-funcs MY_PV="${PV/_p/.}.0" MY_P="${PN}-${MY_PV}" DESCRIPTION="Publication-quality molecular visualization package" -HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" + +# Original page dead +#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +HOMEPAGE=" + http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html + http://pjf.net/science/molmol.html +" SRC_URI=" ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2 + https://dev.gentoo.org/~pacho/${PN}/${PN}.png +" LICENSE="molmol" SLOT="0" KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" IUSE="" -DEPEND=" +RDEPEND=" || ( ( media-libs/mesa x11-libs/libGLw ) media-libs/mesa[motif] ) - media-libs/libpng:0 + media-libs/libpng:0= media-libs/tiff:0 sys-libs/zlib virtual/glu virtual/jpeg:0 x11-libs/libXpm x11-libs/motif:0 - x11-apps/xdpyinfo" -RDEPEND="${DEPEND}" + x11-apps/xdpyinfo +" +DEPEND="${RDEPEND}" +BDEPEND="" S="${WORKDIR}" @@ -44,12 +53,14 @@ pkg_setup() { } src_prepare() { + default + rm -rf tiff* # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff + eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - epatch "${WORKDIR}"/patches/ldflags.patch - epatch "${WORKDIR}"/patches/opengl.patch + eapply "${WORKDIR}"/patches/ldflags.patch + eapply "${WORKDIR}"/patches/opengl.patch ln -s makedef.lnx "${S}"/makedef || die @@ -62,14 +73,14 @@ src_prepare() { -e "s:^CC.*:CC = $(tc-getCC):" \ -i "${S}"/makedef || die - epatch "${WORKDIR}"/patches/cast.patch - epatch "${WORKDIR}"/patches/libpng15.patch + eapply "${WORKDIR}"/patches/cast.patch + eapply -p0 "${WORKDIR}"/patches/libpng15.patch # patch from fink # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${WORKDIR}"/patches/${P}-fink.patch + eapply "${WORKDIR}"/patches/${P}-fink.patch - epatch "${WORKDIR}"/patches/wild.patch + eapply "${WORKDIR}"/patches/wild.patch tc-export AR } @@ -81,5 +92,9 @@ src_install() { insinto ${MMDIR} doins -r auxil help macros man setup tips - dodoc HISTORY README + make_desktop_entry "${PN}" + doicon "${DISTDIR}/${PN}.png" + + einstalldocs + dodoc HISTORY } diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 1bbeb6cfbd8e..53adcde9c072 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,8 +1,6 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c -DIST pymol-2.2.0.tar.gz 10514753 BLAKE2B 54bf7c639ec1af0c318438f6dcbe5878aded5cc360dee3a5f1dee4b6eea588f4242865ae8adf1e044628ad5f71aa8f6d58d0cc71baf7c1f20eed3045ed3a1cb1 SHA512 56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133 DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe EBUILD pymol-1.8.4.0-r1.ebuild 3009 BLAKE2B a076dd994e90f886e65cbb5b3f976e75eacd0a6f153c1b9417c476b53d2169495b08b6d3361ab5fcb55102a2e93a86b7f0ac6d0f25bca947f6b13f52dadde6bd SHA512 c696905b2e28c28249bf458e37dfe05237b307e3af1727fe17ebfd6a818322e6f9dc947d720df7ee29d694fe6501791f3a2f6fdc554a8e7dd43adf9727c8ece8 -EBUILD pymol-2.2.0.ebuild 3123 BLAKE2B d5d39aca27089614f5f095eaef2d89bc783f1b3144a944b5e03fa80c2eb3a15402a6041dbe7e59af8c04e9b5e4668d93073cc6173495079f803537485390830c SHA512 4c6a01df6417ea2e28f1a90a2e690b078b853e7bfc4d42f418a095ae605b7fcd316b57e201e1b0debcd15fb8102f9c6e20e7a0a7067af3e1f4372eef76faa635 -EBUILD pymol-2.3.0.ebuild 3142 BLAKE2B d03631d7794b9557c6dcac84895bb0a10766a97a5b81a93ce2a54f8b6d89c0f27f2249109e51c8a8f315948786ba6f49f716f23810d438c36de9fd1237c11de4 SHA512 c90b2798a36403c316f36a483fbc2887d84e55afea4667704543c388a5803ed678830276c4621b7499fb759ea67a29545c399acdea4d88a1c22feb9b31ca2aeb +EBUILD pymol-2.3.0-r1.ebuild 3134 BLAKE2B 5dac0f4ca3041d02d27d9484bd3a6fe9ac037ffd367e36308ace5c6e5b3389c42cdcde5939c3a5af03f782ebb2fee994547e3251747e02f1c2df610dda17f9f1 SHA512 2fdffad45d70aa2117f295027701ebb2c6d6b523c939caf2c4d128f40e557d118377a5e93612ce1db247341509740274c8520af9f11d121cf66bb502565229d5 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 diff --git a/sci-chemistry/pymol/pymol-2.2.0.ebuild b/sci-chemistry/pymol/pymol-2.2.0.ebuild deleted file mode 100644 index 1e53d9ab3397..000000000000 --- a/sci-chemistry/pymol/pymol-2.2.0.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit distutils-r1 eutils xdg-utils flag-o-matic - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="http://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -# git archive -v --prefix=${P}/ master -o ${P}.tar.xz -RESTRICT="mirror" -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="web" - -DEPEND=" - dev-libs/msgpack[cxx] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pyopengl[${PYTHON_USEDEP}] - media-libs/freeglut - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - virtual/python-pmw[${PYTHON_USEDEP}] - !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -e "/import/s:argparse:argparseX:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - sed \ - -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1d' \ - -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ - -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ - -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - - python_foreach_impl python_doscript "${T}"/${PN} - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry ${PN} PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} - -pkg_postinst() { - xdg_desktop_database_update - xdg_mimeinfo_database_update - optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -} - -pkg_postrm() { - xdg_desktop_database_update - xdg_mimeinfo_database_update -} diff --git a/sci-chemistry/pymol/pymol-2.3.0.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild index 0f1975780234..89aef82c8e96 100644 --- a/sci-chemistry/pymol/pymol-2.3.0.ebuild +++ b/sci-chemistry/pymol/pymol-2.3.0-r1.ebuild @@ -4,9 +4,8 @@ EAPI=7 PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" -inherit distutils-r1 eutils xdg-utils flag-o-matic +inherit distutils-r1 desktop eutils flag-o-matic xdg-utils DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="http://www.pymol.org/" @@ -14,7 +13,6 @@ SRC_URI=" https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz " -# git archive -v --prefix=${P}/ master -o ${P}.tar.xz RESTRICT="mirror" LICENSE="PSF-2.2" SLOT="0" @@ -26,7 +24,8 @@ DEPEND=" dev-libs/mmtf-cpp dev-python/numpy[${PYTHON_USEDEP}] dev-python/pyopengl[${PYTHON_USEDEP}] - media-libs/freeglut + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] media-libs/freetype:2 media-libs/glew:0= media-libs/glm diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index 72040c83b5ce..e170171ba4f4 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,9 +1,11 @@ -AUX vmd-1.9.1-cuda-device_ptr.patch 934 BLAKE2B c0a6f938df4f9ac8d85bc147d83904deb5c3e93d7912a11a75e31a91029d7319228b0cffc09b9e154957e9d8d148089628de262e8d30d7acab5637951d5d25b0 SHA512 274756fe17fdcc39ce471c3187f3076407d34b64e49b0006ee30525a952277b2b5c713fffa8786162dc542eef2b021f2bf7339736cf9e81b673d5146114829ed +AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d +AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00 DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba EBUILD vmd-1.9.2.ebuild 7155 BLAKE2B 734137c1a02d76da109d35faf11f29138a8e48dda6d84b7151f93f2095481127f136a5f8954a80912c85ae7031a01c3374783a042bf5461fd9d1049b577a082b SHA512 3f9fc1f4cc8f6f5031de74a8211db2a9e11d07de110689832d408c343a307ba25efa354f5862d4e6d8d06d3d18b567820401fc9fcdc8818f65a33ea24a3c657b +EBUILD vmd-1.9.3-r1.ebuild 7512 BLAKE2B cfd3259efcf3457e520f8f9ebf809373a99b6d6d5d3ab36192bf7ddd694835d7dd5c113957591d9041b583e58ac419f6cb8649f24ded0e62c89cabf056d45020 SHA512 cb0fc6cbc37c39351d51a3535569adaa69f4aee81942c0eeb83fbd7f1ca5aa3005bc8c87a74002869cc4fd81fb917601ae1bfd0a3dfd474fcf345f696cfd7d21 EBUILD vmd-1.9.3.ebuild 7110 BLAKE2B d8ad6f495aaacdc4727e2c0e5d950a9670478aba7b55e62ed7074f06ad26151468f0f55a0786ce9dba80a181e7c36e912eaeaaa9ad7ae660739c65f482337c97 SHA512 c0eba398b6a815a59c9d8708dc796273ad3211ddc8e02aee8333f00f42f095c4d8999aaa246665ceb9282d2053c0631dc3c8ed7b60981d88ff9f8a2badf6b89a MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9 diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch index ce842448decf..67eb11bbd36b 100644 --- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch +++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch @@ -4,8 +4,8 @@ diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu index 5bfe7bf..36faaf0 100755 ---- a/vmd-1.9.1/src/CUDAMarchingCubes.cu -+++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu +--- a/src/CUDAMarchingCubes.cu ++++ b/src/CUDAMarchingCubes.cu @@ -45,6 +45,7 @@ #include "CUDAMarchingCubes.h" #include <thrust/scan.h> @@ -16,8 +16,8 @@ index 5bfe7bf..36faaf0 100755 // (limited by shared memory size) diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu index a21ebde..56a42c8 100755 ---- a/vmd-1.9.1/src/CUDAQuickSurf.cu -+++ b/vmd-1.9.1/src/CUDAQuickSurf.cu +--- a/src/CUDAQuickSurf.cu ++++ b/src/CUDAQuickSurf.cu @@ -22,6 +22,7 @@ #include <stdlib.h> #include <string.h> diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch new file mode 100644 index 000000000000..b71cd97210a8 --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch @@ -0,0 +1,13 @@ +--- a/configure.old 2019-05-16 17:26:05.347560700 +0200 ++++ b/configure 2019-05-16 17:30:25.478455770 +0200 +@@ -1105,8 +1105,8 @@ + # This may be commented out if not required. + $libtachyon_defines = "-DVMDLIBTACHYON"; + $libtachyon_dir = "$vmd_library_dir/tachyon"; +-$libtachyon_include = "-I$libtachyon_dir/include"; +-$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; ++$libtachyon_include = "-Igentoo-libtachyon-include"; ++$libtachyon_library = "-Lgentoo-libtachyon-libs"; + $libtachyon_libs = "-ltachyon"; + @libtachyon_cc = (); + @libtachyon_cu = (); diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild new file mode 100644 index 000000000000..3f24f85d6273 --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild @@ -0,0 +1,262 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz + ${P}.src.tar +" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.6.1:0= + dev-lang/perl + dev-libs/expat + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + ${PYTHON_DEPS} + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama ) +" +DEPEND="${CDEPEND}" +BDEPEND=" + virtual/pkgconfig + dev-lang/swig +" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) +" + +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 ${P}.src.tar from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" + elog "Place both into your DISTDIR directory" + elog + elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" + elog "file may get downloaded as a compressed tarball or not. In that case" + elog "you will need to ensure you uncompress the file and rename it" + elog "as ${P}.src.tar" +} + +src_prepare() { + default + + use cuda && cuda_sanitize + + eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch + + cd "${WORKDIR}"/plugins || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.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}" || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch + eapply "${FILESDIR}"/${P}-configure-libtachyon.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.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} |