Commit ab7b72cb authored by Edlira Nano's avatar Edlira Nano
Browse files

changed changelog + debian files + doc

git-svn-id: https://subversion.renater.fr/masschroq/trunk@1993 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 40326b9d
quantimscpp (0.0.6-1) jaunty; urgency=low
masschroq (1.0.0-1) maverick; urgency=low
* xsd schema fixed
* no search on simple peptides where isotope labels are used
* sax parser fixed for type argument (alignment and detection methods)
* bug fixed parsing detection_zivy and detection_moulon tags
* conversion of retention times to "hh:mm:ss.zzz"
* split gnumeric result in 2 sheets
[ Edlira Nano ]
* Initial release.
-- Olivier Langella <olivier.langella@moulon.inra.fr> Fri, 05 Mar 2010 12:18:51 +0200
quantimscpp (0.0.5-2) jaunty; urgency=low
* moc cxx files problem fixed in the package
-- Olivier Langella <olivier.langella@moulon.inra.fr> Mon, 24 Apr 2009 12:18:51 +0200
quantimscpp (0.0.5-1) jaunty; urgency=low
* peak detection fixed by Benoit Valot
* xml outputs float with higher precision (10)
-- Olivier Langella <olivier.langella@moulon.inra.fr> Mon, 24 Apr 2009 10:18:51 +0200
quantimscpp (0.0.4-1) intrepid; urgency=low
* handles suspend to disk for huge msrun data
-- Olivier Langella <olivier.langella@moulon.inra.fr> Mon, 03 Apr 2009 10:18:51 +0200
quantimscpp (0.0.3-1) intrepid; urgency=low
* xicextractor works
* background substraction works
* GUI now allow to choose a mass precisely
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Mon, 16 Mar 2009 16:18:51 +0200
quantimscpp (0.0.2-1) intrepid; urgency=low
* new object to align ms runs
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 30 Jan 2009 16:18:51 +0200
quantimscpp (0.0.1-3) intrepid; urgency=low
* licence added in the package for src/libobiwarp (Copyright (c) 2006, The University of Texas at Austin("U.T. Austin"))
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 23 Jan 2009 16:18:51 +0200
quantimscpp (0.0.1-2) intrepid; urgency=low
* fixed binary installation in package.
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 23 Jan 2009 15:18:51 +0200
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
-- enano <enano@moulonadm-desktop> Mon, 14 Feb 2011 17:27:14 +0100
......@@ -5,12 +5,12 @@ Maintainer: 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: quilt, cdbs, debhelper (>= 5), cmake (>= 2.6), pkg-config (>= 0.22), libqt4-dev (>= 4.5.2), libqwt5-qt4-dev (>= 5)
Build-Depends: quilt, cdbs, debhelper (>= 5), cmake (>= 2.6), pkg-config (>= 0.22), libqt4-dev (>= 4.5.2)
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
Package: masschroq
Architecture: any
Depends: ${shlibs:Depends}, libqwt5-qt4 (>= 5)
Depends: ${shlibs:Depends}, libqt4 (>= 4.5.2)
Description: Mass Chromatogram Quantification
MassChroQ (Mass Chromatogram Quantification) software performs quantification
of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques.
......
......@@ -48,8 +48,8 @@ install: build
dh_clean -k
dh_installdirs
# Add here commands to install the package into debian/quantimscpp.
$(MAKE) DESTDIR=$(CURDIR)/debian/quantimscpp install
# Add here commands to install the package into debian/masschroq.
$(MAKE) DESTDIR=$(CURDIR)/debian/masschroq install
# Build architecture-independent files here.
......
......@@ -57,6 +57,8 @@
\newcommand{\bi}{\begin{itemize}}
\newcommand{\ei}{\end{itemize}}
\newcommand{\bverb}{\begin{verbatim}}
\newcommand{\everb}{\end{verbatim}}
\newcommand{\M}{MassChroQ}
\newcommand{\Pa}{\emph{PAPPSO}}
\newcommand{\Mv}{MassChroQ v.1.0}
......@@ -110,7 +112,6 @@
\newcommand{\twist}{\sigma}
\newcommand{\twistv}{\tilde{\sigma}}
\newcommand{\lamv}{\tilde{\lambda}}
\newcommand{\ev}{\mathsf{ev}}
\newcommand{\comp}{\mathsf{c}}
\newcommand{\du}{\mathsf{d}}
\newcommand{\uu}{\mathsf{u}}
......@@ -180,14 +181,17 @@ format data.
{\M} is an open-source software released under the
\href{http://www.gnu.org/licenses/gpl.html}{Gnu General Public Licence
v3.0}. It is developped at the \href{http://pappso.inra.fr/}{PAPPSO} team
version 3}. It is developped at the \href{http://pappso.inra.fr/}{PAPPSO} team
(??? ajouter le moulon ou pas ?\href{http://moulon.inra.fr/}{INRA Moulon})
On the \href{http://pappso.inra.fr/masschroq}{{\M} homepage}
On the \href{http://pappso.inra.fr/masschroq/}{{\M} homepage}
you will find executables, a FAQ, and the latest news about the project.
On the \href{http://sourcesup.cru.fr/projects/masschroq/}{{\M}
development page} you will find a bug tracker and various forums.
The source code is anonymously available via the subversion repository
at \href{}{SourceSup}.
at \url{https://subversion.cru.fr/masschroq/}.
This manual contains detailed information about the concepts and
features of {\Mv}. It is intended to provide all the
......@@ -198,8 +202,10 @@ technical information needed for an advanced comprehension and use.
% ici résumé des possibilités techniques de MassChroQ pas très
%détaillées, une phrase, mais il faut tout mettre
Quantification of data obtained from LC-MS is the main scope of
{\M}. To achieve this {\M} can combine and perform the following features :
{\M} has been designed to perform quantification on a wide range of
LC-MS data: label-free or isotopic labeled ones,
high-resolution (HR) or low-resolution (LR) ones.
To achieve this {\M} can combine and perform the following features :
\begin{itemize}
\item Grouping of LC-MS data that present biological affinities (for
example grouping of the same LC fractions in an SCX separated set
......@@ -236,12 +242,12 @@ an LR LTQ spectrometer which produces a certain baseline noise but no
spikes. We can group the Orbitrap runs together and put the LTQ ones in another
group. We then apply a quantification method containing an anti-spike
XIC filter to the first group, and another quantification method containing
a background filter to the latter. The quantification results will be
sumarized in a single file, sorted by group and sample, allowing
a background filter to the latter and tell masschroq to perform
analysis in both groups in one shot.The quantification results will be
summarized in a single file, sorted by group and sample, allowing
comparisons to be performed easily.
To summarize, analysis in MassChroQ is performed by groups of samples,
which allow a certain flexibility and performance: for example XICs
Thus, groups allow a certain flexibility and performance: for example XICs
for a given peptide are only extracted in groups where the MS/MS
allowed its identification.
......@@ -257,7 +263,7 @@ Two different alignment algorithms are implemented in {\M} :
The following XIC filters are implemented in {\M} :
\begin{itemize}
\item background filter : a median filter follwed by an opening filter,
\item background filter : a median filter followed by an opening filter,
\item smoothing filter : a moving average filter,
\item anti-spike filter.
\end{itemize}
......@@ -270,8 +276,9 @@ The following peak-detection techniques are possible in {\M} :
morphological filtering of the signal that allows a reliable peak detection.
\end{itemize}
{\M} accepts mzXML and mzML LC-MS data formats. Also, in order to
include the identified peptides in \M's analysis there are two
{\M} accepts mzXML and mzML LC-MS data formats.
To include the identified peptides in \M's analysis there are two
possibilities :
\begin{itemize}
\item by using the open-source tool
......@@ -284,17 +291,42 @@ possibilities :
\subsection{Installation and help}
The svn repository is located ???
\subsubsection*{Linux platforms}
An Ubuntu package is available ???
You need Qt 4.5.2 or higher to build {\mexe} on Linux. Most Linux distributions
have packages named libqt4-dev available. In any case, be sure to get
the -dev package for Qt in addition to any other libraries.
\subsubsection*{Windows platforms}
The Windows binary is available ???
\begin{itemize}
\item Ubuntu : {\M} is available from the repository :
\url{https://launchpad.net/~olivier-langella/+archive/ppa}.
To add it to your sources list use the following commands:
\begin{verbatim}
sudo add-apt-repository ppa:olivier-langella/ppa
sudo apt-get update
\end{verbatim} and then install it with Synaptic or by typing :
\begin{verbatim}
sudo apt-get install masschroq
\end{verbatim}
\item Others ???
\end{itemize}
\subsubsection*{Windows platforms}
A win32 executable is available at : \url{???}.
??? recommandations.
\subsubsection*{SVN repository}
The subversion repository located at
\url{https://subversion.cru.fr/masschroq/} is available read-only to
the public at large. Assuming you have at least version 1.0.0 of
\href{http://subversion.tigris.org/}{Subversion} installed, you can
checkout {\M} sources using the following command :
\begin{verbatim}
svn checkout https://subversion.cru.fr/masschroq/ some_local_directory.
\end{verbatim}
\subsubsection*{Further documentation}
\subsubsection*{Help}
On the {\M} homepage (http://pappso.inra.fr/masschroq) you
will find :
......@@ -481,7 +513,7 @@ above example we have defined group \ttt{G1} containing data
\mylst{11}{14}
In the \ttt{<peptide_files_list>} block the user defines
In the \ttt{<peptide\_files\_list>} block the user defines
line 11 - line 33 : here are the results of the identification
process : the list of peptides, proteins and isotopes identified
......
/*
*
* MassChroQ: Mass Chromatogram Quantification software.
* Copyright (C) 2010 Olivier Langella, Edlira Nano, Benoit Valot, Michel Zivy.
*
* 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/>.
*
*/
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