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add clustalx

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starsareintherose 2021-11-01 17:33:04 +00:00
parent c2979ebf28
commit bf7abebea5
5 changed files with 307 additions and 0 deletions
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28
clustalx/0001-fix-qt.patch Executable file
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@ -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 <vector>
-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 <QtGui>
#include "Resources.h"
-const string HelpDisplayWidget::helpFileName = "clustalx.hlp";
+const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
HelpDisplayWidget::HelpDisplayWidget(char helpPointer)
{

200
clustalx/0002-fix-qt.patch Executable file
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@ -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 <QtGui>
#include <QPushButton>
#include <QGroupBox>
#include <QCheckBox>
@@ -20,8 +21,8 @@
#include <QGridLayout>
#include <QSizePolicy>
#include <QComboBox>
-#include <QtGui>
#include <QLabel>
+#include <QLineEdit>
#include <iostream>
#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 <QFontMetrics>
+#include <QVBoxLayout>
+#include <QScrollBar>
+#include <QScrollArea>
+#include <QMessageBox>
+#include <QGroupBox>
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 <QtGui>
+#include <QScrollArea>
#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 <QtGui>
#include <QPushButton>
#include <QGroupBox>
#include <QCheckBox>
@@ -12,8 +13,8 @@
#include <QGridLayout>
#include <QSizePolicy>
#include <QComboBox>
-#include <QtGui>
#include <QLabel>
+#include <QLineEdit>
#include <iostream>
#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 <QtGui>
+#include <QMessageBox>
#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 <QTextEdit>
#include <iostream>
#include <fstream>
+#include <QPushButton>
+#include <QVBoxLayout>
#include <QtGui>
#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 <iomanip>
#include <sstream>
#include <QtGui>
+#include <QMessageBox>
#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 <QLabel>
#include <QString>
#include <QMessageBox>
+#include <QLineEdit>
#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 <QComboBox>
#include <QtGui>
#include <QLabel>
+#include <QMessageBox>
+#include <QLineEdit>
#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 <QtGui>
+#include <QScrollArea>
#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 <QComboBox>
#include <QtGui>
#include <QLabel>
+#include <QLineEdit>
#include <iostream>
#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 <QComboBox>
#include <QtGui>
#include <QLabel>
+#include <QLineEdit>
+#include <QMessageBox>
#include <iostream>
#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 <cstdlib>
#include <QCheckBox>
#include <QStringList>
+#include <QMenu>
+#include <QMenuBar>
+#include <QAction>
+#include <QMessageBox>
+#include <QApplication>
+#include <QScrollBar>
+#include <QHBoxLayout>
+#include <QGroupBox>
+#include <QVBoxLayout>
#include "SecStructOptions.h"
#include "mainwindow.h"
#include "WritePostscriptFile.h"

57
clustalx/PKGBUILD Executable file
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@ -0,0 +1,57 @@
# Maintainer: Hu Butui <hot123tea123@gmail.com>
# Contributor: Matt Neilson <ichthyoboy at gmail dot com>
# Contributor: Mick Elliot <micke at sfu dot ca>
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:

12
clustalx/lilac.py Executable file
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@ -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:

10
clustalx/lilac.yaml Executable file
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@ -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: