From 80208fb578cf92cc308906660ca6d7860c6b2a1f Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 9 Mar 2018 16:53:27 +0000 Subject: gentoo resync : 09.03.2018 --- sci-biology/Manifest.gz | Bin 25448 -> 25460 bytes sci-biology/amos/Manifest | 2 +- sci-biology/amos/amos-3.1.0-r3.ebuild | 53 ---- sci-biology/amos/amos-3.1.0-r4.ebuild | 52 ++++ sci-biology/clustalx/Manifest | 2 + sci-biology/clustalx/clustalx-2.1-r3.ebuild | 56 ++++ sci-biology/clustalx/files/clustalx-2.1-qt5.patch | 295 ++++++++++++++++++++++ 7 files changed, 406 insertions(+), 54 deletions(-) delete mode 100644 sci-biology/amos/amos-3.1.0-r3.ebuild create mode 100644 sci-biology/amos/amos-3.1.0-r4.ebuild create mode 100644 sci-biology/clustalx/clustalx-2.1-r3.ebuild create mode 100644 sci-biology/clustalx/files/clustalx-2.1-qt5.patch (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index ec4f5e09ff11..d3e2e55bcd81 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest index cf9af10bddd2..0749a737c777 100644 --- a/sci-biology/amos/Manifest +++ b/sci-biology/amos/Manifest @@ -4,5 +4,5 @@ AUX amos-3.1.0-goBambus2.py-indent-and-cleanup.patch 1057 BLAKE2B fde1011da76275 AUX amos-3.1.0-qa-Wformat.patch 4511 BLAKE2B 64064175db625a098a528f0c8036196968c58dae445edd3c98fc5627e3a84d593abc438958573ef7a28193d0d2fc76db30fe16a180a383dec9bae5084305505d SHA512 de0382f9128b46fef8e87d14de75bbc9f0af3e8bcbb915edab26a883186109ab29ddbb31c5cf70fc8d37700abe36fb73a7bdca46c29672052d01ebebffd52abe DIST amos-3.1.0-fix-c++14.patch.bz2 8033 BLAKE2B 942248f64906253205392df71010bf41105d2985fc8112e7443975d776cc484a4e2b6cf34284d4c384145bf32601892c06f156a0b0ccf0f2ce721de242e02e9b SHA512 76e26ca48a009cbf637d9462878223633e9b21cbd12d58a19e9a561f2cf4805791becc0b5f7aaf81975ca1e02b263cdd9d5ff310c4594670922ea65885ad9634 DIST amos-3.1.0.tar.gz 2094268 BLAKE2B b9fb80d4e7b7e9e7769081c2680a3cba26591f00a4d9fdb17ad602e581dea5e8e2add4b0d9d3821a7f8a4ec1a45dfd867037baf35ecd401584f030c86b2b0f83 SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 -EBUILD amos-3.1.0-r3.ebuild 1189 BLAKE2B d0e36265d14eb3b3c0da7e21edc63bc75e3176d52ec0a117fefa394d234f29954809626bd0517a9210b7fa104dae9c72f962b3cde12386da04890f039a5af8a2 SHA512 b2e0386fc5bd65884f4f9ccbdb74ec0f42c37c157cf52c17195fbf390156f242f9c77780323b40fa33e6f5be52863fb0beddd23048695c3e40a65f2272dce7c7 +EBUILD amos-3.1.0-r4.ebuild 1110 BLAKE2B 4730d6a04ba727fd72ea825c6c57d65079ae9ddb29411f0a26aa94653309364ddec742104783044549adc2a60f06a7452f76e392145aa02db472042dde05e1d5 SHA512 7cb40d45dabc4e6cc188d3edf8347f34578d1f955b2d522273f3b551be6974023145e35a443f0e4495d70746aa40b6c451cedf999c102f1f8f7ffbab09748d61 MISC metadata.xml 345 BLAKE2B 750928cf3e96c24e2af8e84d5889100c1954eb140596368dc00d479f63898c82e3bb0e07a9e970c6c12eb36ed3ae84c6bcc7913cf3ed56e2d71120185d24a4f0 SHA512 a31ba5660e524b70517f2644bb929d4bc0428d1ea682752ca2ddefd3b5a8a5c8aabf7a9877fa61e8fe12599da65e9f0a6c1e7db90d61729e26c33b76303ff497 diff --git a/sci-biology/amos/amos-3.1.0-r3.ebuild b/sci-biology/amos/amos-3.1.0-r3.ebuild deleted file mode 100644 index 33c30995b11b..000000000000 --- a/sci-biology/amos/amos-3.1.0-r3.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 qmake-utils - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz - https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="qt4" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="qt4? ( dev-qt/qtcore:4 )" -RDEPEND="${DEPEND} - ${PYTHON_DEPS} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -PATCHES=( - "${FILESDIR}"/${P}-gcc-4.7.patch - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch - "${WORKDIR}"/${P}-fix-c++14.patch - "${FILESDIR}"/${P}-qa-Wformat.patch - "${FILESDIR}"/${P}-fix-build-system.patch -) - -src_prepare() { - default - eautoreconf - - # prevent GCC 6 log pollution due - # to hash_map deprecation in C++11 - append-cxxflags -Wno-cpp -} - -src_configure() { - econf \ - --with-qmake-qt4=$(usex qt4 $(qt4_get_bindir)/qmake no) -} - -src_install() { - default - python_fix_shebang "${ED%/}"/usr/bin/goBambus2 -} diff --git a/sci-biology/amos/amos-3.1.0-r4.ebuild b/sci-biology/amos/amos-3.1.0-r4.ebuild new file mode 100644 index 000000000000..0dbcaffd81da --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r4.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools flag-o-matic python-single-r1 + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-3.1.0-fix-c++14.patch.bz2" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="" +RDEPEND="${DEPEND} + ${PYTHON_DEPS} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch + "${WORKDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-qa-Wformat.patch + "${FILESDIR}"/${P}-fix-build-system.patch +) + +src_prepare() { + default + eautoreconf + + # prevent GCC 6 log pollution due + # to hash_map deprecation in C++11 + append-cxxflags -Wno-cpp +} + +src_configure() { + econf --with-qmake-qt4=no +} + +src_install() { + default + python_fix_shebang "${ED%/}"/usr/bin/goBambus2 +} diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest index 7d3cf91d5636..aae876b740a0 100644 --- a/sci-biology/clustalx/Manifest +++ b/sci-biology/clustalx/Manifest @@ -1,5 +1,7 @@ +AUX clustalx-2.1-qt5.patch 8173 BLAKE2B dca2d4f7531ac38510cc9c2aa788244293c436940d38945c906c76b7a29d395179190833517c01cbe48d450111d3f115427fb55536ab55dd01fc0617ff9e7bc2 SHA512 d8c9e9e1aade86f6ba4aa88618ace305152b819cf445119c82b4d4e56c7923e25876c83fd74c8dc91715ce484ff0ea3111b13ed7d8219c1222ad60e09b72d29e DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864bd55a9fe37eb68c0b36ae89e07848e8fdae2207ff9b3850eebc273b803df0261eefd3e7d96d8fa58c75af3adc SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a EBUILD clustalx-2.1-r1.ebuild 1093 BLAKE2B 369910c48ad315148d210bf616980a483ca37ec9a27e227876e4057faed667db1ca4bc8dfd760dcce2ccb1d54a3fa7d4fdf3d762bdc7b89908c8bdcbcd2610e6 SHA512 997c71482dff6f73841ba912904b9ea34992ffd9dc90466e233017857a93c11a2f930ff242bfc0b1309bedbf4e6be2556bf26efa9a9f7dfe83d0e96abc06e8a0 EBUILD clustalx-2.1-r2.ebuild 1225 BLAKE2B 458fb581439821d8eabffc507148a830a74e593f84679757699348d65f1bbe076e5fcba21f0fd2d083256d0de63498378ab87f4a3d74d5f3166fbddd93437954 SHA512 6d0d46521bc2511dca32363e7faf6ff550de74f6e6fcf22f0d3ebd7cbe0f10884dbdb52fcfcba034b4185419d2109663bf1e589d072937b6bbc012fe5ad5c250 +EBUILD clustalx-2.1-r3.ebuild 1336 BLAKE2B 0116719c2b776feedeaae20148ee41c5b8cc1d3ddcb006f1899f0db198d2c8e8ab4b8dc8813a806775c367db2a863df769032f02e35584c3aadef78c60f1f90f SHA512 587d03c86f6faf24bbb49cbc9328923fd9d9634a1bd2360669d1c2e25329ad996c6bc63c717af044fc816f009bab482953a5efcb0d11adff161664da930b1fc6 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild new file mode 100644 index 000000000000..0f9366bee7f5 --- /dev/null +++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit desktop qmake-utils + +DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" +HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +SRC_URI=" + http://www.clustal.org/download/current/${P}.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtwidgets:5 + dev-qt/qtxml:5 +" +RDEPEND="${DEPEND} + >=sci-biology/clustalw-${PV} +" + +PATCHES=( "${FILESDIR}/${P}"-qt5.patch ) # kindly borrowed from Debian + +src_prepare() { + default + sed \ + -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \ + -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \ + -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \ + -i ClustalQtParams.h || \ + die "Failed to patch shared files location." + sed \ + -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ + -i HelpDisplayWidget.cpp || \ + die "Failed to patch help file location." + rm -rf usr || die +} + +src_configure() { + eqmake5 +} + +src_install() { + dobin clustalx + insinto /usr/share/${PN} + doins colprot.xml coldna.xml colprint.xml clustalx.hlp + make_desktop_entry ${PN} ClustalX + doicon "${WORKDIR}"/${PN}.png +} diff --git a/sci-biology/clustalx/files/clustalx-2.1-qt5.patch b/sci-biology/clustalx/files/clustalx-2.1-qt5.patch new file mode 100644 index 000000000000..96b108c14474 --- /dev/null +++ b/sci-biology/clustalx/files/clustalx-2.1-qt5.patch @@ -0,0 +1,295 @@ +Author: Andreas Tille +Last-Update: Mon, 11 Sep 2017 09:30:38 +0200 +Description: Porting to Qt5 following the hints at + https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#QtWidgets_as_a_Separate_Module + https://wiki.qt.io/Transition_from_Qt_4.x_to_Qt5#toAscii.28.29_and_fromAscii.28.29_Methods_are_deprecated + +--- a/clustalx.pro ++++ b/clustalx.pro +@@ -6,6 +6,7 @@ TEMPLATE = app + TARGET = clustalx + CONFIG += release static + QT += xml ++QT += widgets + VERSION = 2.1 + win32 { + DEFINES += OS_WINDOWS +--- a/AlignOutputFileNames.cpp ++++ b/AlignOutputFileNames.cpp +@@ -20,7 +20,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "AlignOutputFileNames.h" +--- a/AlignmentFormatOptions.cpp ++++ b/AlignmentFormatOptions.cpp +@@ -5,7 +5,7 @@ + #include + #include + #include +-#include ++#include + #include + #include "AlignmentFormatOptions.h" + #include "clustalW/general/userparams.h" +--- a/AlignmentParameters.cpp ++++ b/AlignmentParameters.cpp +@@ -11,7 +11,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include +--- a/AlignmentViewerWidget.cpp ++++ b/AlignmentViewerWidget.cpp +@@ -60,7 +60,7 @@ + *****************************************************************************/ + + +-#include ++#include + #include + #include + #include "AlignmentViewerWidget.h" +--- a/AlignmentWidget.cpp ++++ b/AlignmentWidget.cpp +@@ -45,7 +45,7 @@ + * + ****************************************************************************/ + +-#include ++#include + #include "AlignmentWidget.h" + #include "clustalW/general/userparams.h" + #include "ClustalQtParams.h" +--- a/BootstrapTreeDialog.cpp ++++ b/BootstrapTreeDialog.cpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "BootstrapTreeDialog.h" +--- a/ColorFileXmlParser.cpp ++++ b/ColorFileXmlParser.cpp +@@ -1,4 +1,4 @@ +-#include ++#include + + #include "ColorFileXmlParser.h" + #include "ClustalQtParams.h" +--- a/ColumnScoreParams.cpp ++++ b/ColumnScoreParams.cpp +@@ -11,7 +11,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include +--- a/HelpDisplayWidget.cpp ++++ b/HelpDisplayWidget.cpp +@@ -16,7 +16,7 @@ + #include + #include + #include +-#include ++#include + #include "Resources.h" + + const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp"; +--- a/HistogramWidget.cpp ++++ b/HistogramWidget.cpp +@@ -21,7 +21,7 @@ + ****************************************************************************/ + + #include "HistogramWidget.h" +-#include ++#include + #include + //#include + #include +--- a/LowScoringSegParams.cpp ++++ b/LowScoringSegParams.cpp +@@ -12,7 +12,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include +--- a/PSPrinter.cpp ++++ b/PSPrinter.cpp +@@ -16,7 +16,7 @@ + #include + #include + #include +-#include ++#include + #include "PSPrinter.h" + #include "ColorFileXmlParser.h" + #include "clustalW/general/userparams.h" +@@ -594,7 +594,7 @@ void PSPrinter::printHeaderLine(ofstream + { + psX = blockLeft + (i - fr) * CHARWIDTH; + (*psOutFile) << "("; +- (*psOutFile) << data->seqHeader[ix][i].toAscii(); ++ (*psOutFile) << data->seqHeader[ix][i].toLatin1(); + (*psOutFile) << ") "; + (*psOutFile) << psX << " " << psY << " " << psX << " " + << psY << " 1.0 1.0 1.0 color_inv\n"; +--- a/PairwiseParams.cpp ++++ b/PairwiseParams.cpp +@@ -18,7 +18,7 @@ + #include + #include + #include +-#include ++#include + #include "clustalW/general/userparams.h" + #include "clustalW/substitutionMatrix/globalmatrix.h" + #include "FileDialog.h" +--- a/ProteinGapParameters.cpp ++++ b/ProteinGapParameters.cpp +@@ -5,7 +5,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include +--- a/SaveSeqFile.cpp ++++ b/SaveSeqFile.cpp +@@ -18,7 +18,7 @@ + #include + #include + #include +-#include ++#include + #include + #include "SaveSeqFile.h" + #include "clustalW/general/userparams.h" +--- a/SecStructOptions.cpp ++++ b/SecStructOptions.cpp +@@ -5,7 +5,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "SecStructOptions.h" +--- a/SeqNameWidget.cpp ++++ b/SeqNameWidget.cpp +@@ -55,7 +55,7 @@ + * + ****************************************************************************/ + +-#include ++#include + #include "SeqNameWidget.h" + #include "KeyController.h" //- nige + #include "clustalW/alignment/Alignment.h" +--- a/TreeFormatOptions.cpp ++++ b/TreeFormatOptions.cpp +@@ -4,7 +4,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "TreeFormatOptions.h" +--- a/TreeOutputFileNames.cpp ++++ b/TreeOutputFileNames.cpp +@@ -11,7 +11,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "TreeOutputFileNames.h" +--- a/WritePostscriptFile.cpp ++++ b/WritePostscriptFile.cpp +@@ -18,7 +18,7 @@ + #include + #include + #include +-#include ++#include + #include + #include + #include "WritePostscriptFile.h" +--- a/mainwindow.cpp ++++ b/mainwindow.cpp +@@ -87,7 +87,7 @@ + * + ****************************************************************************/ + +-#include ++#include + #include + #include + #include +--- a/ColorParameters.cpp ++++ b/ColorParameters.cpp +@@ -154,8 +154,8 @@ QColor ColorParameters::getResidueColor( + { + int i, j; + QChar colorParRes; +- char showRes = res.toAscii(); +- char showCon = consensus.toAscii(); ++ char showRes = res.toLatin1(); ++ char showCon = consensus.toLatin1(); + + for(i = 0; i < colorPar.size(); i++) + { +@@ -171,7 +171,7 @@ QColor ColorParameters::getResidueColor( + + for(j = 0; j < colorPar[i].consensusConditionList.size(); j++) + { +- char temp = colorPar[i].consensusConditionList[j].toAscii(); ++ char temp = colorPar[i].consensusConditionList[j].toLatin1(); + if(consensus == colorPar[i].consensusConditionList[j]) + { + return colorPar[i].color; +@@ -191,8 +191,8 @@ int ColorParameters::getResidueColorNum( + { + int i, j; + QChar colorParRes; +- char showRes = res.toAscii(); +- char showCon = consensus.toAscii(); ++ char showRes = res.toLatin1(); ++ char showCon = consensus.toLatin1(); + + for(i = 0; i < colorPar.size(); i++) + { +@@ -208,7 +208,7 @@ int ColorParameters::getResidueColorNum( + + for(j = 0; j < colorPar[i].consensusConditionList.size(); j++) + { +- char temp = colorPar[i].consensusConditionList[j].toAscii(); ++ char temp = colorPar[i].consensusConditionList[j].toLatin1(); + if(consensus == colorPar[i].consensusConditionList[j]) + { + return getIndexOfColor(colorPar[i].color); -- cgit v1.2.3