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Commit 9c61f7de authored by Langella Olivier's avatar Langella Olivier
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Merge branch 'master' of forgemia.inra.fr:pappso/masschroq

parents 27c13eb4 bfa6a5f6
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.gitignore
View file @ 9c61f7de
build
src/config.h
templates/share/applications/masschroq-gui.desktop
templates/share/applications/masschroq-studio.desktop
.project
*~
CMakeLists.txt
View file @ 9c61f7de
......@@ -132,17 +132,12 @@ endif( CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo" )
message(STATUS "${BoldYellow}CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}.${ColourReset}")
#depending on libpappsomspp version :
set(LIBPAPPSOMSPP_VERSION "0.8.3")
configure_file (${CMAKE_SOURCE_DIR}/debian/control.cmake ${CMAKE_SOURCE_DIR}/debian/control @ONLY)
# Project version
#
SET (MASSCHROQ_MAJOR_VERSION 2)
SET (MASSCHROQ_MINOR_VERSION 2)
SET (MASSCHROQ_PATCH_LEVEL 22)
SET (MASSCHROQ_PATCH_LEVEL 23)
SET (MASSCHROQ_VERSION
"${MASSCHROQ_MAJOR_VERSION}.${MASSCHROQ_MINOR_VERSION}.${MASSCHROQ_PATCH_LEVEL}")
SET (MASSCHROQ_LIB_NAME "masschroq")
......@@ -151,8 +146,7 @@ SET (MASSCHROQ_LIB_SOVERSION ${MASSCHROQ_MAJOR_VERSION})
SET (MASSCHROQ_SCHEMA_VERSION "${MASSCHROQ_MAJOR_VERSION}.2")
#SET (masschroq_BINARY_DIR "bin")
SET(VERSION 2.2.23)
# We want C++17
......
CMakeStuff/modules/convert_svg.bash
View file @ 9c61f7de
......@@ -7,6 +7,6 @@ FILES=$@
for f in $FILES
do
echo " file : $f"
inkscape --without-gui --export-pdf="${f%.svg}.pdf" $f
echo "Converting svg file $f to pdf file ${f%.svg}.pdf"
convert $f ${f%.svg}.pdf
done
CMakeStuff/toolchains/unix-toolchain.cmake
View file @ 9c61f7de
......@@ -6,26 +6,18 @@ set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
if (NOT OdsStream_FOUND)
find_package( OdsStream REQUIRED )
endif (NOT OdsStream_FOUND)
find_package(OdsStream REQUIRED)
if (NOT PappsoMSpp_FOUND)
find_package ( PappsoMSpp REQUIRED )
endif (NOT PappsoMSpp_FOUND)
find_package(PappsoMSpp COMPONENTS Core Widget REQUIRED)
#find_package( Boost COMPONENTS iostreams thread filesystem chrono REQUIRED )
find_package( Boost COMPONENTS thread filesystem iostreams REQUIRED )
if(PappsoMSpp_FOUND)
message(STATUS "PappsoMSpp and PappsoMSppWidget were found at: ${PappsoMSpp_LIBRARY}")
message(STATUS "Include dir for PappsoMSpp is at: ${PappsoMSpp_INCLUDE_DIRS}")
endif()
set(Alglib_DIR ${CMAKE_MODULE_PATH})
find_package(Alglib REQUIRED)
find_package( ZLIB REQUIRED )
set(Zstd_DIR ${CMAKE_MODULE_PATH})
find_package(Zstd REQUIRED)
find_package( QCustomPlot REQUIRED )
buildwin32.cmd deleted 100644 → 0
View file @ 27c13eb4
rem Dependency paths:
set CMAKE=C:\Program Files\CMake 2.6\bin\cmake.exe
rem used for headers only; we get the lib from the libpng build
rem set ZLIBDIR=c:\developer\lib\zlib
rem provides both png and zlib .libs
rem set PNGDIR=C:\developer\lib\lpng1220-vc\
set QTDIR=C:\Qt\4.8.6\
set QWT_ROOT=C:\qwt-5.2.3
set QT_PLUGIN_PATH="${QWT_ROOT}\designer\plugins\designer:$QT_PLUGIN_PATH"
rem set CAIRODIR=C:\developer\lib\cairo-1.6.0
rem set LCMSDIR=c:\developer\lib\lcms-1.16-vc
rem set JPEGDIR=c:\developer\lib\jpeg-6b-vc
rem set FREETYPEDIR=c:\developer\lib\freetype-2.3.5
rem set TIFFDIR=c:\developer\lib\tiff-3.8.2-vc
rem set PODOFODIR=c:\developer\podofo\050-vs-inst
rem set PODOFOSHARED=1
rem set LIBXMLDIR=c:\developer\lib\libxml2-2.6.30.win32
rem set SCRIBUSINSTALLDIR=c:\developer\scribus-bin
rem
rem
set PATH=C:\mingw32\bin;C:\Qt\4.8.6\bin;C:\Qt\4.8.6\plugins\designer;%PATH%
set
rem set PATH=%SYSTEMROOT%;%SYSTEMROOT%\system32;%QTDIR%\bin
set INCLUDE=
set LIB=
rem set SCPNGPROJ=%PNGDIR%\projects\visualc71\
del cmakecache.txt
rem %CMAKE%" -G "MinGW Makefiles" -DCMAKE_INCLUDE_PATH:PATH=%QTDIR%\src\3rdparty\zlib;%QTDIR%\src\3rdparty\libpng;%ZLIBDIR%;%ZLIBDIR%\include;%PNGDIR%;%PNGDIR%\include;%CAIRODIR%;%CAIRODIR%\include;%LCMSDIR%\include;%JPEGDIR%;%JPEGDIR%\include;%TIFFDIR%\libtiff;%TIFFDIR%\include;%FREETYPEDIR%\include;%FREETYPEDIR%\include\freetype2;%PODOFODIR%\include;%LIBXMLDIR%\include -DCMAKE_LIBRARY_PATH:PATH=%ZLIBDIR%\lib;%SCPNGPROJ%\Win32_DLL_Debug\Zlib;%SCPNGPROJ%\Win32_DLL_Release\Zlib;%PNGDIR%\lib;%SCPNGPROJ%\Win32_DLL_Debug;%SCPNGPROJ%\Win32_DLL_Release;%LCMSDIR%\lib;%LCMSDIR%\Lib\MS;%LCMSDIR%\Lib\MS\dll;%JPEGDIR%;%JPEGDIR%\lib;%TIFFDIR%\libtiff;%TIFFDIR%\lib;%FREETYPEDIR%\objs;%FREETYPEDIR%\lib;%PODOFODIR%\lib;%LIBXMLDIR%\lib -DCMAKE_INSTALL_PREFIX=c:\
\ No newline at end of file
debian/changelog
View file @ 9c61f7de
masschroq (2.2.23-1) unstable; urgency=low
* New upstream release that will correspond to the first upload to the
debian servers (NEW queue).
* [Filippo Rusconi]
- Updates to the packaging to make it comply with Debian standards.
-- Filippo Rusconi <lopippo@debian.org> Wed, 02 Dec 2020 14:23:02 +0100
masschroq (2.2.22-4) buster; urgency=medium
* new PAPPSOms++ library
......
debian/control 0 → 100644
View file @ 9c61f7de
Source: masschroq
Section: science
Priority: optional
Maintainer: Olivier Langella <olivier.langella@u-psud.fr>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper-compat (= 12),
dh-exec (>= 0.3),
dpkg-dev (>= 1.18.25),
cmake (>= 3.12),
libx11-dev,
libc6-dev,
qtbase5-dev,
libqt5xmlpatterns5-dev,
texlive-latex-extra,
texlive-latex-recommended,
texlive-fonts-recommended,
texlive-science,
hevea,
latex2html,
poppler-utils,
graphicsmagick-imagemagick-compat,
doxygen,
graphviz,
libpappsomspp-dev (>= 0.8.11),
libpappsomspp-widget-dev (>= 0.8.11),
libodsstream-dev (>= 0.7.9),
libqcustomplot-dev(>= 2.0)
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/debichem-team/masschroq
Vcs-Git: https://salsa.debian.org/debichem-team/masschroq.git
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
Package: masschroq-cli
Architecture: linux-any
Depends: ${shlibs:Depends},
${misc:Depends},
Suggests: masschroq-gui,
masschroq-doc
Description: Mass Chromatogram Quantification - command line interface
The MassChroQ software performs quantification of data obtained from LC-MS
(liquid chromatography - mass spectrometry) experiments.
.
In particular it can be used to perform:
- retention-time alignment of runs
- XIC extraction and filtering
- peak detection and quantification.
peak detection and quantification.
.
This package ships the command line interface program.
Package: masschroq-gui
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
masschroq-cli (= ${binary:Version})
Suggests: masschroq-doc
Description: Mass Chromatogram Quantification - graphical user interface
The MassChroQ software performs quantification of data obtained from LC-MS
(liquid chromatography - mass spectrometry) experiments.
.
In particular it can be used to perform:
- retention-time alignment of runs
- XIC extraction and filtering
- peak detection and quantification.
peak detection and quantification.
.
This package ships the graphical user interface programs.
Package: masschroq-condor
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
htcondor
Suggests: masschroq-cli
masschroq-gui,
masschroq-doc
Description: Mass Chromatogram Quantification - condor Perl script
The MassChroQ software performs quantification of data obtained from LC-MS
(liquid chromatography - mass spectrometry) experiments.
.
In particular it can be used to perform:
- retention-time alignment of runs
- XIC extraction and filtering
- peak detection and quantification.
peak detection and quantification.
.
This package ships a Perl script to launch MassChroQ via the condor job queue.
Package: masschroq-doc
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: masschroq-cli
masschroq-gui,
Description: Mass Chromatogram Quantification - documentation
The MassChroQ software performs quantification of data obtained from LC-MS
(liquid chromatography - mass spectrometry) experiments.
.
In particular it can be used to perform:
- retention-time alignment of runs
- XIC extraction and filtering
- peak detection and quantification.
peak detection and quantification.
.
This package ships the MassChroQ documentation.
debian/control.cmake deleted 100644 → 0
View file @ 27c13eb4
Source: masschroq
Section: science
Priority: optional
Maintainer: Olivier Langella <olivier.langella@u-psud.fr>
Uploaders: Olivier Langella <olivier.langella@u-psud.fr>
DM-Upload-Allowed: yes
Standards-Version: 3.9.1.0
Build-Depends: debhelper (>= 5),
cmake (>= 2.6),
libx11-dev,
libc6-dev,
texlive-latex-extra,
texlive-latex-recommended,
texlive-fonts-recommended,
texlive-science,
hevea,
inkscape,
doxygen,
libpappsomspp-dev (>= @LIBPAPPSOMSPP_VERSION@),
libpappsomspp-widget-dev (>= @LIBPAPPSOMSPP_VERSION@),
libpappsomspp-widget0 (>= @LIBPAPPSOMSPP_VERSION@),
libodsstream-dev (>= 0.7.9),
qtbase5-dev,
libqcustomplot-dev,
libqt5xmlpatterns5-dev
Build-Conflicts: qt3-dev-tools
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
Package: masschroq-common
Architecture: linux-any
Depends: ${shlibs:Depends},
${misc:Depends},
libqt5core5a,
libqt5concurrent5,
libpappsomspp0 (>= @LIBPAPPSOMSPP_VERSION@),
libodsstream0 (>= 0.7.9)
Replaces: masschroq (<< 1.5.0)
Conflicts: masschroq (<< 1.5.0)
Suggests: masschroq, masschroq-gui, masschroq-studio
Description: Mass Chromatogram Quantification shared libraries
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Package: masschroq-doc
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: masschroq,
masschroq-gui,
masschroq-studio
Description: Mass Chromatogram Quantification documentation
Installs PDF documentation for MassChroQ in /usr/share/doc/masschroq
Package: masschroq
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
masschroq-common (= ${binary:Version}),
libqt5core5a,
libqt5xml5
Suggests: xtpcpp,
masschroq-doc,
masschroq-gui,
masschroq-studio
Description: Mass Chromatogram Quantification CLI (Command Line Interface)
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Package: masschroq-gui
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
masschroq-common (= ${binary:Version}),
libqt5core5a,
libqt5gui5,
libqt5concurrent5,
libqt5network5
Suggests: masschroq-doc, masschroq-studio
Description: Mass Chromatogram Quantification graphical user interface
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Package: masschroq-studio
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
masschroq-common (= ${binary:Version}),
libpappsomspp-widget0 (>= @LIBPAPPSOMSPP_VERSION@),
libqt5core5a,
libqt5gui5,
libqt5xml5
Suggests: masschroq-doc, masschroq-gui
Description: Mass Chromatogram Quantification graphical user interface to edit parameters
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Package: masschroq-condor
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
masschroq,
htcondor
Suggests: masschroq-doc,
masschroq-gui,
masschroq-studio
Description: Perl script to launch MassChroQ via condor job queue
Perl script to launch MassChroQ via condor job queue
debian/copyright
View file @ 9c61f7de
......@@ -3,20 +3,17 @@ Upstream-Name: masschroq
Source: http://pappso.inra.fr/bioinfo/masschroq/
Files: *
Copyright: 2011 Olivier Langella <olivier.langella@moulon.inra.fr>
Copyright: 2011-2020 Olivier Langella <olivier.langella@moulon.inra.fr>
Edlira Nano <edlira.nano@moulon.inra.fr>
Benoît Valot <benoit.valot@moulon.inra.fr>
Michel Zivy <michel.zivy@moulon.inra.fr>
License: GPL-3.0+
Files: debian/*
Copyright: 2011 Edlira Nano <edlira.nano@moulon.inra.fr>
License: GPL-3.0+
Files: src/libobiwarp/*
Copyright: Copyright (c) 2006, The University of Texas at
Austin("U.T. Austin"). All rights reserved.
License:
License: expat-like
Software by John T. Prince under the direction of Edward M. Marcotte.
By using this software the USER indicates that he or she has read,
understood and will comply with the following:
......@@ -45,6 +42,12 @@ License:
Submit software operation questions to: Edward M. Marcotte, Department
of Chemistry and Biochemistry, U. T. Austin, Austin, Texas 78712.
Files: debian/*
Copyright: 2011 Edlira Nano <edlira.nano@moulon.inra.fr>
2020 Filippo Rusconi <lopippo@debian.org>
License: GPL-3.0+
Licence: GPL-3.0+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
......@@ -61,3 +64,4 @@ Licence: GPL-3.0+
.
On Debian systems, the full text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
debian/masschroq-common.install deleted 100644 → 0
View file @ 27c13eb4
/usr/lib/*/masschroq/libmasschroq.*
/usr/share/masschroq/masschroq.svg
debian/masschroq-gui.install
View file @ 9c61f7de
/usr/bin/masschroq_studio
/usr/share/applications/masschroq-studio.desktop
/usr/bin/masschroq_gui
/usr/share/applications/masschroq-gui.desktop
\ No newline at end of file
/usr/share/applications/masschroq-gui.desktop
debian/masschroq-studio.install deleted 100644 → 0
View file @ 27c13eb4
/usr/bin/masschroq_studio
/usr/share/applications/masschroq-studio.desktop
\ No newline at end of file
debian/masschroq.install deleted 100644 → 0
View file @ 27c13eb4
/usr/bin/masschroq
\ No newline at end of file
debian/rules 100644 → 100755
View file @ 9c61f7de
......@@ -6,8 +6,7 @@
export DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
%:
dh $@ --buildsystem=cmake --parallel
# dh $@ --buildsystem=cmake --parallel
dh $@ --buildsystem=cmake
override_dh_auto_configure:
dh_auto_configure -- -DLIB_SUFFIX="/$(DEB_HOST_MULTIARCH)" -DCMAKE_INSTALL_PREFIX=/usr -DGO_LATEX=true -DCMAKE_BUILD_TYPE=Release
......
debian/upstream/metadata 0 → 100644
View file @ 9c61f7de
Reference:
- Author: Benoît Valot and Olivier Langella and Edlira Nano and Michel Zivy
Title: >
MassChroQ: a versatile tool for mass spectrometry quantification
Journal: Proteomics
Year: 2011
Month: 09
Volume: 11
Number: 17
Pages: 3572-3577
DOI: 10.1002/pmic.201100120
PMID: 21751374
URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201100120
ePrint: https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201100120
Repository : https://forgemia.inra.fr/pappso/masschroq
src/CMakeLists.txt
View file @ 9c61f7de
......@@ -9,17 +9,13 @@ find_package( Qt5 COMPONENTS Core Gui Xml XmlPatterns Widgets Concurrent PrintSu
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/modules)
#if (RocksDB_FOUND)
#else (RocksDB_FOUND)
# FIND_PACKAGE( RocksDB REQUIRED )
#endif (RocksDB_FOUND)
if (QCustomPlot_FOUND)
else (QCustomPlot_FOUND)
find_package( QCustomPlot REQUIRED )
endif (QCustomPlot_FOUND)
if (OdsStream_FOUND)
else (OdsStream_FOUND)
find_package( OdsStream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
......@@ -28,25 +24,23 @@ endif (OdsStream_FOUND)
#sudo apt-get install libpappsomspp-dev
if (PappsoMSpp_FOUND)
else (PappsoMSpp_FOUND)
if(PappsoMSpp_FOUND)
else(PappsoMSpp_FOUND)
message("looking for PAPPSOms++ library")
find_package( PappsoMSpp REQUIRED )
endif (PappsoMSpp_FOUND)
endif(PappsoMSpp_FOUND)
if (PappsoMSpp_FOUND)
else (PappsoMSpp_FOUND)
if(PappsoMSpp_FOUND)
else(PappsoMSpp_FOUND)
message("PAPPSOms++ library not found")
message("did you apt-get install libpappsomspp-dev ?")
endif (PappsoMSpp_FOUND)
endif(PappsoMSpp_FOUND)
if (PappsoMSppWidget_FOUND)
else (PappsoMSppWidget_FOUND)
if(PappsoMSppWidget_FOUND)
else(PappsoMSppWidget_FOUND)
message("PAPPSOms++ widget library not found")
message("did you apt-get install libpappsomspp-widget-dev ?")
endif (PappsoMSppWidget_FOUND)
endif(PappsoMSppWidget_FOUND)
set (GUI_UIS
......@@ -222,9 +216,6 @@ target_link_libraries(masschroq_main ${MASSCHROQ_LIB_NAME}
PappsoMSpp::Core
PappsoMSpp::Widget
OdsStream::Core
Boost::thread
Boost::filesystem
Boost::iostreams
Qt5::Core
)
set_target_properties(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
......@@ -243,9 +234,6 @@ else (NOGUI)
Qt5::Core
Qt5::Gui
Qt5::Widgets
Boost::thread
Boost::filesystem
Boost::iostreams
)
add_executable(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS})
......@@ -257,10 +245,7 @@ else (NOGUI)
Qt5::Gui
Qt5::Widgets
Qt5::PrintSupport
${QCustomPlot_LIBRARIES}
Boost::thread
Boost::filesystem
Boost::iostreams
${QCustomPlot_LIBRARIES}
)
endif (NOGUI)
......
src/config.h 0 → 100644
View file @ 9c61f7de
#ifndef _CONFIG_H
#define _CONFIG_H
#define SOFTWARE_NAME "MassChroQ"
#define MASSCHROQ_VERSION "2.2.23"
#define MASSCHROQ_XSD "masschroq-2.2.xsd"
#define MASSCHROQ_SCHEMA_VERSION "2.2"
#define MASSCHROQ_SCHEMA_FILE \
":/resources/schema/masschroq-2.2.xsd"
/* #undef MASSCHROQ_ICON */
#define QT_V_4_5 0x040500
#define QT_V_4_6 0x040600
#include <QDebug>
#include "mcq_types.h"
#endif /* _CONFIG_H */
templates/share/applications/masschroq-gui.desktop 0 → 100644
View file @ 9c61f7de
[Desktop Entry]
Name=MassChroQ GUI 2.2.23
Categories=Education;Science;Math;
Comment=MassChroQ GUI launcher
Exec=masschroq_gui %U
Icon=/usr/share/masschroq/masschroq.svg
Terminal=false
Type=Application
StartupNotify=true
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