From bf7abebea5b3b6c04eb5f6304a73c865ab3799bb Mon Sep 17 00:00:00 2001 From: starsareintherose Date: Mon, 1 Nov 2021 17:33:04 +0000 Subject: [PATCH] add clustalx --- clustalx/0001-fix-qt.patch | 28 ++++++ clustalx/0002-fix-qt.patch | 200 +++++++++++++++++++++++++++++++++++++ clustalx/PKGBUILD | 57 +++++++++++ clustalx/lilac.py | 12 +++ clustalx/lilac.yaml | 10 ++ 5 files changed, 307 insertions(+) create mode 100755 clustalx/0001-fix-qt.patch create mode 100755 clustalx/0002-fix-qt.patch create mode 100755 clustalx/PKGBUILD create mode 100755 clustalx/lilac.py create mode 100755 clustalx/lilac.yaml diff --git a/clustalx/0001-fix-qt.patch b/clustalx/0001-fix-qt.patch new file mode 100755 index 0000000000..a23f0018c4 --- /dev/null +++ b/clustalx/0001-fix-qt.patch @@ -0,0 +1,28 @@ +diff -urN clustalx-2.1/ClustalQtParams.h clustalx-2.1a/ClustalQtParams.h +--- clustalx-2.1/ClustalQtParams.h 2010-11-17 05:12:30.000000000 -0500 ++++ clustalx-2.1a/ClustalQtParams.h 2010-11-18 12:19:42.450866697 -0500 +@@ -13,9 +13,9 @@ + #include "clustalW/alignment/Alignment.h" + #include + +-static QString psColorFile = "colprot.xml"; +-static QString psDNAFile = "coldna.xml"; +-static QString psPrintFile = "colprint.xml"; ++static QString psColorFile = "/usr/share/clustalx/colprot.xml"; ++static QString psDNAFile = "/usr/share/clustalx/coldna.xml"; ++static QString psPrintFile = "/usr/share/clustalx/colprint.xml"; + + static const int BlackAndWhite = 1; + static const int ColorsBackGround = 2; +diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1a/HelpDisplayWidget.cpp +--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 05:12:30.000000000 -0500 ++++ clustalx-2.1a/HelpDisplayWidget.cpp 2010-11-18 12:20:34.727866697 -0500 +@@ -19,7 +19,7 @@ + #include + #include "Resources.h" + +-const string HelpDisplayWidget::helpFileName = "clustalx.hlp"; ++const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp"; + + HelpDisplayWidget::HelpDisplayWidget(char helpPointer) + { diff --git a/clustalx/0002-fix-qt.patch b/clustalx/0002-fix-qt.patch new file mode 100755 index 0000000000..72907ea824 --- /dev/null +++ b/clustalx/0002-fix-qt.patch @@ -0,0 +1,200 @@ +diff -urN clustalx-2.1/AlignOutputFileNames.cpp clustalx-2.1-bak/AlignOutputFileNames.cpp +--- clustalx-2.1/AlignOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignOutputFileNames.cpp 2015-09-18 18:59:38.582405761 +0200 +@@ -13,6 +13,7 @@ + * 18-06-07,Nigel Brown(EMBL): Made the 'ok' button in each dialogue be the + * default instead of a Browse button. + */ ++#include + #include + #include + #include +@@ -20,8 +21,8 @@ + #include + #include + #include +-#include + #include ++#include + #include + #include "AlignOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/AlignmentViewerWidget.cpp clustalx-2.1-bak/AlignmentViewerWidget.cpp +--- clustalx-2.1/AlignmentViewerWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentViewerWidget.cpp 2015-09-18 18:50:09.762563103 +0200 +@@ -69,6 +69,11 @@ + #include "PSPrinter.h" + #include "FileDialog.h" + #include ++#include ++#include ++#include ++#include ++#include + + AlignmentViewerWidget::AlignmentViewerWidget(QWidget *parent) + : QWidget(parent), +diff -urN clustalx-2.1/AlignmentWidget.cpp clustalx-2.1-bak/AlignmentWidget.cpp +--- clustalx-2.1/AlignmentWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/AlignmentWidget.cpp 2015-09-18 18:58:36.656119118 +0200 +@@ -46,6 +46,7 @@ + ****************************************************************************/ + + #include ++#include + #include "AlignmentWidget.h" + #include "clustalW/general/userparams.h" + #include "ClustalQtParams.h" +diff -urN clustalx-2.1/BootstrapTreeDialog.cpp clustalx-2.1-bak/BootstrapTreeDialog.cpp +--- clustalx-2.1/BootstrapTreeDialog.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/BootstrapTreeDialog.cpp 2015-09-18 19:00:09.782214298 +0200 +@@ -5,6 +5,7 @@ + * 12-4-07, Mark Larkin, Removed destructor. No need to delete QObjects. Also removed + * setAllPtrsToNull function. + */ ++#include + #include + #include + #include +@@ -12,8 +13,8 @@ + #include + #include + #include +-#include + #include ++#include + #include + #include "BootstrapTreeDialog.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ColorFileXmlParser.cpp clustalx-2.1-bak/ColorFileXmlParser.cpp +--- clustalx-2.1/ColorFileXmlParser.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ColorFileXmlParser.cpp 2015-09-18 19:00:42.695345653 +0200 +@@ -1,4 +1,5 @@ + #include ++#include + + #include "ColorFileXmlParser.h" + #include "ClustalQtParams.h" +@@ -202,4 +203,4 @@ + rule = rule.nextSiblingElement("resrule"); + } + return numOfRules; +-} +\ No newline at end of file ++} +diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1-bak/HelpDisplayWidget.cpp +--- clustalx-2.1/HelpDisplayWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/HelpDisplayWidget.cpp 2015-09-18 19:34:51.692771579 +0200 +@@ -16,6 +16,8 @@ + #include + #include + #include ++#include ++#include + #include + #include "Resources.h" + +diff -urN clustalx-2.1/PSPrinter.cpp clustalx-2.1-bak/PSPrinter.cpp +--- clustalx-2.1/PSPrinter.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/PSPrinter.cpp 2015-09-18 19:20:36.528019466 +0200 +@@ -17,6 +17,7 @@ + #include + #include + #include ++#include + #include "PSPrinter.h" + #include "ColorFileXmlParser.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/ProteinGapParameters.cpp clustalx-2.1-bak/ProteinGapParameters.cpp +--- clustalx-2.1/ProteinGapParameters.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/ProteinGapParameters.cpp 2015-09-18 19:20:07.311532091 +0200 +@@ -9,6 +9,7 @@ + #include + #include + #include ++#include + #include "ProteinGapParameters.h" + #include "clustalW/general/userparams.h" + +diff -urN clustalx-2.1/SaveSeqFile.cpp clustalx-2.1-bak/SaveSeqFile.cpp +--- clustalx-2.1/SaveSeqFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SaveSeqFile.cpp 2015-09-18 19:21:28.231035513 +0200 +@@ -20,6 +20,8 @@ + #include + #include + #include ++#include ++#include + #include "SaveSeqFile.h" + #include "clustalW/general/userparams.h" + #include "clustalW/general/utils.h" +diff -urN clustalx-2.1/SeqNameWidget.cpp clustalx-2.1-bak/SeqNameWidget.cpp +--- clustalx-2.1/SeqNameWidget.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/SeqNameWidget.cpp 2015-09-18 19:22:48.903873782 +0200 +@@ -56,6 +56,7 @@ + ****************************************************************************/ + + #include ++#include + #include "SeqNameWidget.h" + #include "KeyController.h" //- nige + #include "clustalW/alignment/Alignment.h" +diff -urN clustalx-2.1/TreeOutputFileNames.cpp clustalx-2.1-bak/TreeOutputFileNames.cpp +--- clustalx-2.1/TreeOutputFileNames.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/TreeOutputFileNames.cpp 2015-09-18 19:23:37.006911921 +0200 +@@ -13,6 +13,7 @@ + #include + #include + #include ++#include + #include + #include "TreeOutputFileNames.h" + #include "clustalW/general/userparams.h" +diff -urN clustalx-2.1/WritePostscriptFile.cpp clustalx-2.1-bak/WritePostscriptFile.cpp +--- clustalx-2.1/WritePostscriptFile.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/WritePostscriptFile.cpp 2015-09-18 19:24:30.429917414 +0200 +@@ -20,6 +20,8 @@ + #include + #include + #include ++#include ++#include + #include + #include "WritePostscriptFile.h" + #include "clustalW/general/userparams.h" +Binary files clustalx-2.1/clustalx and clustalx-2.1-bak/clustalx differ +diff -urN clustalx-2.1/clustalx.pro clustalx-2.1-bak/clustalx.pro +--- clustalx-2.1/clustalx.pro 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/clustalx.pro 2015-09-18 19:14:42.666857671 +0200 +@@ -4,8 +4,11 @@ + + TEMPLATE = app + TARGET = clustalx +-CONFIG += release static ++CONFIG += release + QT += xml ++QT += widgets ++DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x000000 ++ + VERSION = 2.1 + win32 { + DEFINES += OS_WINDOWS +diff -urN clustalx-2.1/mainwindow.cpp clustalx-2.1-bak/mainwindow.cpp +--- clustalx-2.1/mainwindow.cpp 2010-11-17 11:12:30.000000000 +0100 ++++ clustalx-2.1-bak/mainwindow.cpp 2015-09-18 19:19:03.545256739 +0200 +@@ -94,6 +94,15 @@ + #include + #include + #include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include + #include "SecStructOptions.h" + #include "mainwindow.h" + #include "WritePostscriptFile.h" diff --git a/clustalx/PKGBUILD b/clustalx/PKGBUILD new file mode 100755 index 0000000000..1f8ab74b07 --- /dev/null +++ b/clustalx/PKGBUILD @@ -0,0 +1,57 @@ +# Maintainer: Hu Butui +# Contributor: Matt Neilson +# Contributor: Mick Elliot + +pkgname=clustalx +pkgver=2.1 +pkgrel=2 +pkgdesc='Multiple alignment of nucleic acid and protein sequences (command line tool' +arch=('x86_64') +url='http://www.clustal.org/clustal2' +license=('LGPL3') +depends=( + qt5-base +) +makedepends=( + gendesk +) +source=("${pkgname}-${pkgver}.tar.gz::http://www.clustal.org/download/current/clustalx-${pkgver}.tar.gz" + "0001-fix-qt.patch" + "0002-fix-qt.patch" + "${pkgname}.png::http://www.clustal.org/images/clustalw_title.png" +) +sha256sums=('e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05' + '5c070a5cd2e7ba5eddf984b6d5ad2bdbb1dc5fd1c50edaefd109e094ed33431c' + '8a5bd0329015d70e2e649c33c13aaabbb88999305f83f4c0fa0c01fe1af3db72' + '6444ab0c22ecbefba05b968558eb543dda4c7e0ad140b485832d763e9f8c2dbd') + +prepare() { + cd "${pkgname}-${pkgver}" + patch -p1 -i "${srcdir}/0001-fix-qt.patch" + patch -p1 -i "${srcdir}/0002-fix-qt.patch" + sed -i 's/static//g' clustalx.pro + + echo "Creating desktop file" + gendesk -f -n --pkgname ${pkgname} \ + --pkgdesc "${pkgdesc}" \ + --categories "Graphics;MedicalSoftware;Science;" \ + --icon "${pkgname}" \ + --exec "${pkgname}" +} + +build() { + cd "${pkgname}-${pkgver}" + qmake + make +} + +package() { + cd "${pkgname}-${pkgver}" + install -Dm755 clustalx "${pkgdir}/usr/bin/clustalx" + install -Dm644 colprot.xml "${pkgdir}/usr/share/${pkgname}/colprot.xml" + install -Dm644 coldna.xml "${pkgdir}/usr/share/${pkgname}/coldna.xml" + install -Dm644 coldna.xml "${pkgdir}/usr/share/${pkgname}/colprint.xml" + install -Dm644 clustalx.hlp "${pkgdir}/usr/share/${pkgname}/clustalx.hlp" + install -Dm644 "${srcdir}/${pkgname}.png" "${pkgdir}/usr/share/pixmaps/${pkgname}.png" +} +# vim:set ts=2 sw=2 et: diff --git a/clustalx/lilac.py b/clustalx/lilac.py new file mode 100755 index 0000000000..19737b8d62 --- /dev/null +++ b/clustalx/lilac.py @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 + +from lilaclib import * + + +def pre_build(): + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + +def post_build(): + git_pkgbuild_commit() +# vim:set ts=2 sw=2 et: + diff --git a/clustalx/lilac.yaml b/clustalx/lilac.yaml new file mode 100755 index 0000000000..22d75b3a55 --- /dev/null +++ b/clustalx/lilac.yaml @@ -0,0 +1,10 @@ +maintainers: + - github: starsareintherose + email: starsareintherose@outlook.com +build_prefix: extra-x86_64 +update_on: + - source: regex + url: "http://www.clustal.org/download/current" + regex: 'clustalx-(\d+.\d+)' +# vim:set ts=2 sw=2 et: +