From fbda87924e6faa7a1919f1a2b4182490bde5ec5c Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 3 Sep 2021 20:56:28 +0100 Subject: gentoo resync : 03.09.2021 --- sci-chemistry/Manifest.gz | Bin 10863 -> 10864 bytes sci-chemistry/dssp/Manifest | 8 ++++- sci-chemistry/dssp/dssp-2.2.1-r3.ebuild | 41 ++++++++++++++++++++++++ sci-chemistry/dssp/dssp-3.0.11.ebuild | 42 +++++++++++++++++++++++++ sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild | 33 +++++++++++++++++++ sci-chemistry/dssp/files/30-dssp | 1 + sci-chemistry/dssp/metadata.xml | 7 ++--- 7 files changed, 127 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/dssp/dssp-2.2.1-r3.ebuild create mode 100644 sci-chemistry/dssp/dssp-3.0.11.ebuild create mode 100644 sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild create mode 100644 sci-chemistry/dssp/files/30-dssp (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 8c5226abd681..54ba54961282 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest index e64b097b41a1..12dbd946b77f 100644 --- a/sci-chemistry/dssp/Manifest +++ b/sci-chemistry/dssp/Manifest @@ -1,5 +1,11 @@ +AUX 30-dssp 18 BLAKE2B 3d2b6cfc787c1bec902fca9be8b45bf821f87eb1a0603eab0b537f4ee97a33f61a7fc50aabe85a24d8d5ee48eda6d904db330ade9b71095623afb5df7d83b105 SHA512 a15df4c8b7599a2d6b2575fe02aeb11169ccbd26a70f328cc34b60aee08edabf3cff3d66e5a9c95d06e6630d212a18530ca81aa4004c92fcb461791897bce432 AUX dssp-2.1.0-gentoo.patch 1513 BLAKE2B aabdcfff1083d7552392c35897eb8a84b07323c89dfdce014f4401b2e82e727e9fbc77dd3f7e6d5efda61a6e64fad905873516e5336f21627bda1f2f39caf5c2 SHA512 7d192019811a6892031c74e14ef9fc7461e77c050a164698f8c72cff08f81a0e6da202e0915b631a5cd6d910a6114a736c706d47b1fd6474ff77c3700efcd9f9 AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c13645163478999d5122f09d3a72963843be773210ea225e374941bd057ef6f083a13fb77980bd4390174df2a0c715f0386da7232e0 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 +DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d +DIST dssp-4.0.1_p20210831.tar.gz 121793 BLAKE2B 1e028b086b418772a93db350f8084d1786996ff6ea935d236b1431d8f4a07c0b33ebf374a4c4d5d4d243952f3f56e29a548ce09763863a1e0c529755fba6c211 SHA512 62f1ac781dd3d6f3436e6c155ae1a470d0baf6a6d9f6d6729034a7a5ef41550f76d0473c688d235279336306c9f3598377c056cddd6d00a89a826fbb04c1bfb3 EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926 -MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 +EBUILD dssp-2.2.1-r3.ebuild 882 BLAKE2B 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0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6 diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild new file mode 100644 index 000000000000..8697005fc2cd --- /dev/null +++ b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-libs/boost:=[bzip2,zlib,threads(+)]" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.1.0-gentoo.patch + "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch +) + +src_configure() { + tc-export CXX + + cat >> make.config <<- EOF || die + BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" + BOOST_INC_DIR = "${EPREFIX}/usr/include" + EOF +} + +src_install() { + dobin mkdssp + dosym mkdssp /usr/bin/dssp + doman doc/mkdssp.1 + dodoc README.txt changelog + + doenvd "${FILESDIR}"/30-${PN} +} diff --git a/sci-chemistry/dssp/dssp-3.0.11.ebuild b/sci-chemistry/dssp/dssp-3.0.11.ebuild new file mode 100644 index 000000000000..b0771e31047d --- /dev/null +++ b/sci-chemistry/dssp/dssp-3.0.11.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit autotools + +MY_PN="hssp" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/cmbi/hssp" +SRC_URI="https://github.com/cmbi/${MY_PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-lang/perl:= + dev-libs/boost:=[bzip2,zlib,threads(+)] +" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + default + + # Fix version + sed -i -e "s/3.0.10/${PV}/" configure.ac || die + + sed -i -e '/-Werror/d' Makefile.am || die + + eautoreconf +} + +src_install() { + default + dosym mkdssp /usr/bin/dssp + doenvd "${FILESDIR}"/30-${PN} +} diff --git a/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild new file mode 100644 index 000000000000..a5e5af9c7424 --- /dev/null +++ b/sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +inherit cmake + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp" + +COMMIT="728cc7c6c8d95460d8db453cf7adb25a89ba15f6" +SRC_URI="https://github.com/PDB-REDO/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +BDEPEND=" + >=dev-libs/boost-1.70.0:=[bzip2,zlib,threads(+)] + >=sci-libs/libcifpp-1.1.1 +" +DEPEND="" +RDEPEND="${BDEPEND}" + +pkg_postinst() { + if has_version sci-chemistry/gromacs; then + ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:" + ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129" + ewarn + ewarn "Feel free to mask newer versions if needed." + fi +} diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp new file mode 100644 index 000000000000..e0a5e0ce5626 --- /dev/null +++ b/sci-chemistry/dssp/files/30-dssp @@ -0,0 +1 @@ +DSSP=/usr/bin/dssp \ No newline at end of file diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml index 8937bad0b175..020b40648ee8 100644 --- a/sci-chemistry/dssp/metadata.xml +++ b/sci-chemistry/dssp/metadata.xml @@ -1,8 +1,7 @@ - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - + + pacho@gentoo.org + -- cgit v1.2.3