Commit 614f4caf authored by Edlira Nano's avatar Edlira Nano
Browse files

debian pakage changes

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2197 e4b6dbb4-9209-464b-83f7-6257456c460c
parent e4337379
......@@ -124,11 +124,9 @@ SET(CPACK_SOURCE_IGNORE_FILES
"Makefile"
"install_manifest.txt"
"config.h.cmake"
"cmake_install.cmake"
"CMakeCache.txt"
"CPackConfig.cmake"
"CPackSourceConfig.cmake"
"install_manifest.txt"
"/CMakeFiles/"
"/_CPack_Packages/"
"/Debug/"
......@@ -177,8 +175,8 @@ SET(CPACK_PACKAGE_EXECUTABLES "masschroq" "masschroq")
# for debian package :
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Olivier Langella <olivier.langella@moulon.inra.fr>")
SET(DEBIAN_PACKAGE_BUILDS_DEPENDS "Olivier Langella <olivier.langella@moulon.inra.fr>")
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Edlira Nano <edlira.nano@moulon.inra.fr>")
SET(DEBIAN_PACKAGE_BUILDS_DEPENDS "Edlira Nano <edlira.nano@moulon.inra.fr>")
INCLUDE(CPack)
......@@ -187,11 +185,13 @@ INCLUDE(CPack)
# cause another cmake executable to run. The same process will walk through
# the project's entire directory structure.
add_subdirectory (src)
INSTALL(PROGRAMS src/libmasschroq.so DESTINATION lib)
INSTALL(PROGRAMS src/masschroq DESTINATION bin)
INSTALL(FILES doc/schema/masschroq.xsd DESTINATION share/xml/schema)
INSTALL(FILES doc/man1/masschroq.1.gz DESTINATION share/man/man1)
#INSTALL(FILES doc/man1/masschroq.1.gz DESTINATION share/man/man1)
#INSTALL(FILES doc/manual/masschroq_manual.pdf DESTINATION share/doc/masschroq)
#INSTALL(FILES doc/debian/changelog DESTINATION share/doc/masschroq)
#INSTALL(FILES README DESTINATION share/doc/masschroq)
#INSTALL(PROGRAMS src/viewxic DESTINATION bin)
#INSTALL(PROGRAMS src/align_mzxml DESTINATION bin)
......
......@@ -5,7 +5,7 @@ masschroq (1.1.0-1) unstable; urgency=low
temporary disk files (N is set to 250 Mo but can be configured).
As a result this version uses only 250 Mo of RAM (one slice on memory at a time)
and onlly one msrun is temporary kept on disk at a time. Hence, there is a
gain of more than 50% of execution time and the disk usage is reduced to the
gain of more than 50% of execution time and the disk usage is reduced to the
size of the biggest msrun being analysed.
** Changed the msrun XML parsers: one simple parsing (no spectra) at the beginning
then, when needed, the spectra are parsed. Spectra parsing is needed for the
......@@ -110,4 +110,4 @@ quantimscpp (0.0.1-1) intrepid; urgency=low
* Initial release.
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 23 Jan 2009 11:18:51 +0200
Source: masschroq
Section: science
Priority: optional
Maintainer: Olivier Langella <olivier.langella@moulon.inra.fr>
Maintainer: Edlira Nano <edlira.nano@moulon.inra.fr>
Uploaders: Edlira Nano <edlira.nano@moulon.inra.fr>, Olivier Langella <olivier.langella@moulon.inra.fr>
DM-Upload-Allowed: yes
Uploaders: Olivier Langella <olivier.langella@moulon.inra.fr>
Standards-Version: 3.9.1.0
Build-Depends: debhelper (>= 5), cmake (>= 2.6), libx11-dev, libc6-dev, libqt4-dev (>= 4.5.2)
Build-Depends: debhelper (>= 7.0.50~), cmake (>= 2.6)
Standards-Version: 3.9.1
Build-Conflicts: qt3-dev-tools
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
Package: masschroq
Architecture: any
Depends: ${shlibs:Depends}, libqtcore4 (>= 4.5.2), libqt4-network (>= 4.5.2), libqt4-xmlpatterns (>= 4.5.2), libqt4-xml (>= 4.5.2)
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Mass Chromatogram Quantification
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
In particular it performs : alignment of runs, XIC extraction and filtering,
In particular it performs : retention-time alignment of runs, XIC extraction and filtering,
peak detection and quantification.
Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=REVISION
Upstream-Name: MassChroQ
Uptream-Contact: Olivier Langella <langella@moulon.inra.fr>
Format: http://dep.debian.net/deps/dep5
Upstream-Name: masschroq
Source: http://pappso.inra.fr/bioinfo/masschroq/
Files: *
Copyright: 2011, Olivier Langella <langella@moulon.inra.fr>
Edlira Nano <nano@moulon.inra.fr>
Benoît Valot <valot@moulon.inra.fr>
Michel Zivy <zivy@moulon.inra.fr>
License: GPL-3+
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
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
.
On Debian systems, the full text of the GNU General Public
License version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
Copyright: 2011 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 Olivier Langella <langella@moulon.inra.fr>
License:
Copying and distribution of this package, with or without
modification, are permitted in any medium without royalty
provided the copyright notice and this notice are
preserved.
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: 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:
U. T. Austin hereby grants USER permission to use, copy, modify,
merge, publish, distribute, sublicense, and/or sell copies of this
software and its documentation for any purpose and without fee,
provided that a full copy of this notice is included with the software
and its documentation.
Title to copyright to this software and its associated documentation
shall at all times remain with U. T. Austin. No right is granted to
use in advertising, publicity or otherwise any trademark, service
mark, or the name of U. T. Austin.
This software and any associated documentation are provided "as is,"
and U. T. AUSTIN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESSED OR
IMPLIED, INCLUDING THOSE OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE, OR THAT USE OF THE SOFTWARE, MODIFICATIONS, OR
ASSOCIATED DOCUMENTATION WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS,
TRADEMARKS OR OTHER INTELLECTUAL PROPERTY RIGHTS OF A THIRD
PARTY. U. T. Austin, The University of Texas System, its Regents,
officers, and employees shall not be liable under any circumstances
for any direct, indirect, special, incidental, or consequential
damages with respect to any claim by USER or any third party on
account of or arising from the use, or inability to use, this software
or its associated documentation, even if U. T. Austin has been advised
of the possibility of those damages.
Submit software operation questions to: Edward M. Marcotte, Department
of Chemistry and Biochemistry, U. T. Austin, Austin, Texas 78712.
License:
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:
U. T. Austin hereby grants USER permission to use, copy, modify,
merge, publish, distribute, sublicense, and/or sell copies of this
software and its documentation for any purpose and without fee,
provided that a full copy of this notice is included with the software
and its documentation.
Title to copyright to this software and its associated documentation
shall at all times remain with U. T. Austin. No right is granted to
use in advertising, publicity or otherwise any trademark, service
mark, or the name of U. T. Austin.
This software and any associated documentation are provided "as is,"
and U. T. AUSTIN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESSED OR
IMPLIED, INCLUDING THOSE OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE, OR THAT USE OF THE SOFTWARE, MODIFICATIONS, OR
ASSOCIATED DOCUMENTATION WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS,
TRADEMARKS OR OTHER INTELLECTUAL PROPERTY RIGHTS OF A THIRD
PARTY. U. T. Austin, The University of Texas System, its Regents,
officers, and employees shall not be liable under any circumstances
for any direct, indirect, special, incidental, or consequential
damages with respect to any claim by USER or any third party on
account of or arising from the use, or inability to use, this software
or its associated documentation, even if U. T. Austin has been advised
of the possibility of those damages.
Submit software operation questions to: Edward M. Marcotte, Department
of Chemistry and Biochemistry, U. T. Austin, Austin, Texas 78712.
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
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
.
On Debian systems, the full text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Document: masschroq
Title: Debian MassChroQ Manual
Author: Edlira Nano <edlira.nano@moulon.inra.fr>
Abstract: This manual describes what masschroq is.
Section: unknown
Format: text
Files: /usr/share/doc/masschroq/README
Format: text
Files: /usr/share/doc/masschroq/changelog.Debian
Format: PDF
Files: /usr/share/doc/masschroq/masschroq_manual.pdf
......@@ -45,7 +45,7 @@ clean:
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_prep
dh_installdirs
# Add here commands to install the package into debian/masschroq.
......@@ -60,27 +60,27 @@ binary-indep: build install
binary-arch: build install
dh_testdir
dh_testroot
# dh_installchangelogs ChangeLog
dh_installchangelogs
dh_installdocs
dh_installexamples
# dh_install
# dh_installmenu
# dh_installdebconf
# dh_installlogrotate
# dh_installemacsen
# dh_installpam
# dh_installmime
# dh_python
# dh_installinit
# dh_installcron
# dh_installinfo
dh_install
dh_installmenu
dh_installdebconf
dh_installlogrotate
dh_installemacsen
dh_installpam
dh_installmime
dh_pysupport
dh_installinit
dh_installcron
dh_installinfo
dh_installman
dh_link
dh_strip
dh_compress
dh_fixperms
# dh_perl
# dh_makeshlibs
dh_perl
dh_makeshlibs
dh_installdeb
dh_shlibdeps
dh_gencontrol
......
......@@ -1901,6 +1901,6 @@ retention time is the one used for peak matching. It can be:
%\addtotoc{toc}{Bibliography}
\addcontentsline{toc}{chapter}{\ahrefloc{no:number}{References}}
%\addcontentsline{toc}{chapter}{References}
\bibliography{masschroq_manual-1.0}
\bibliography{masschroq_manual}
\end{document}
......@@ -2,7 +2,7 @@
#define _CONFIG_H
#define MASSCHROQ_VERSION "1.1.0"
#define MASSCHROQ_XSD "/usr/local/share/xml/schema/masschroq.xsd"
#define MASSCHROQ_XSD "/usr/share/xml/schema/masschroq.xsd"
#define MASSCHROQ_XML_VERSION "1.0"
#define QT_V_4_5 0x040500
#define QT_V_4_6 0x040600
......
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