Commit 707727d1 authored by Edlira Nano's avatar Edlira Nano
Browse files

added install manpage into cmakefile + slight modifications to the debian dir

git-svn-id: https://subversion.renater.fr/masschroq/trunk@1930 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 4755b93f
......@@ -154,8 +154,8 @@ add_subdirectory (src)
INSTALL(PROGRAMS src/masschroq DESTINATION bin)
INSTALL(FILES doc/schema/masschroq.xsd DESTINATION share/xml/schema)
INSTALL(DIRECTORY doc/man1/ DESTINATION share/man/man1)
#INSTALL(PROGRAMS src/viewxic DESTINATION bin)
#INSTALL(DIRECTORY doc/man1/maschroq.1 DESTINATION share/man/man1)
#INSTALL(PROGRAMS src/align_mzxml DESTINATION bin)
#INSTALL(PROGRAMS src/xicextractor DESTINATION bin)
Source: quantimscpp
Source: masschroq
Section: science
Priority: optional
Maintainer: Olivier Langella <olivier.langella@moulon.inra.fr>
DM-Upload-Allowed: yes
Uploaders: Olivier Langella <olivier.langella@moulon.inra.fr>
Standards-Version: 0.1
Build-Depends: quilt, cdbs, debhelper (>= 5), cmake (>= 2), pkg-config (>= 0.22), libqt4-dev (>= 4.5.2), libqwt5-qt4-dev (>= 5)
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)
Homepage: http://pappso.inra.fr/bioinfo/masschroq/
Package: quantimscpp
Package: masschroq
Architecture: any
Depends: ${shlibs:Depends}, libqwt5-qt4 (>= 5)
Description: peptide quantitation
peptide quantitation
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,
peak detection and quantification.
X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
X-Debianized-By: Olivier Langella <olivier.langella@moulon.inra.fr>
X-Debianized-Date: Fri, 23 Jan 2009 11:18:51 +0200
X-Source-Downloaded-From:
X-Upstream-Author:
This package wad debianized by OLIVIER LANGELLA <langella@moulon.inra.fr>
on Fri, 23 Jan 2009 11:18:51 +0200
The current debian maintainer is OLIVIER LANGELLA <langella@moulon.inra.fr>
Upstream authors:
Benoît Valot <valot@moulon.inra.fr>
Olivier Langella <langella@moulon.inra.fr>
Edlira Nano <nano@moulon.inra.fr>
Michel Zivy <zivy@moulon.inra.fr>
Files: *
Copyright: © 2008 Olivier Langella <olivier.langella@moulon.inra.fr>
Copyright: © 2010 ...
License: GPL v3
Files: src/libobiwarp/*
......
.TH MASSCHROQ 1 2010-12-21 "version 1.0"
.SH NAME
MassChroQ \- Mass Chromatogram Quantification software
.SH SYNOPSIS
.B masschroq
.I [OPTIONS] [FILE]
.SH DESCRIPTION
.BR MassChroQ
is a powerful tool that performs quantification on data obtained from Liquid
Chromatography\-Mass Spectrometry (LC\-MS) techniques. In particular it performs :
.P
\- alignment of runs (two alignment methods are implemented :
OBI\-Warp alignment method and MS level 2 based alignment method);
.P
\- XIC extraction (and XIC filtering : background filter,
spike removing filter, smoothing filter);
.P
\- peak detection;
.P
\- quantification (of all identified peptides in data and/or of a given
list of m/z values and/or of a given list of m/z\-rt values).
.P
MassChroQ is very flexible and configurable. It takes an XML input
.IR file
where the user defines all the analysis details and their
respective parameters : the raw data files to analyze (mzXML or mzML
files), the different actions to perform on them, the output
quantification result file in different formats (spreadsheets :
gnumeric or tsv, xhtml, xml) and detailed spreadsheet traces files.
The XML input
.I file
can be created by hand (we provide
various complete examples) or automatically by using the X!Tandem pipeline tool
developed in our team. The X!Tandem pipeline automatically includes in
.I file
the list of the identified peptides of your data (using X!Tandem
open-software). Otherwise,
.BR masschroq
can automatically integrate identified peptides into
.I file
by parsing them from peptide text files (tsv or csv text files).
.SH OPTIONS
The following command\-line options are recognized by
.BR masschroq
.TP
.BI \-t,\ \-\-tmpdir \ directory
Use the given
.IR directory
as temporary working directory. By default the system's temporary
directory is used (/tmp on Unix).
.BR masschroq
uses the temporary directory to store
temporary files containing the spectra of the raw LC-MS data being
analyzed. One temporary file per raw data file is
created. These files are automatically deleted on masschroq's exit. If
the total size of the raw data files to analyze is greater than the
system's temporary working directory (~30G on Unix) you should use this
option to specify a directory of your own.
.TP
.BI \-p,\-\-parse\-peptides \ file
Parse the peptide text files (which contain information about identified
peptides) whose path is indicated in the XML input
.IR file
and create a new XML input file named
.IR "parsed-peptides_file"
with the
.IR "file" 's
content plus the parsed peptide information. Then exit without performing other
actions indicated in
.IR "file" .
If this option is not
used and
.IR file
contains peptide text files to parse, the behavior is the same except
that after parsing and creating the parsed-peptides_file masschroq
continues execution on this new file. Thus, this option is useful if
you want to check the parsed peptide information before using it,
or eventually add peptide traces actions into the XML file.
.TP
.B \-h, \-\-help
Print help and exit.
.TP
.B \-v, \-\-version
Print the version number and exit.
.SH "VERSION"
This manual page describes masschroq version 1.0.
.SH "BUGS"
For the list of known masschroq bugs or to report new ones please
visit https://sourcesup.cru.fr/projects/masschroq.
.SH "SEE ALSO"
.TP
.I The MassChroQ user's manual
http://pappso.inra.fr/bioinfo/masschroq/manual
.TP
.I The MassChroQ Homepage
http://pappso.inra.fr/bioinfo/masschroq/
.TP
.I The MassChroQ project page
https://sourcesup.cru.fr/projects/masschroq
.TP
.I The X!Tandem pipeline open\-software
http://pappso.inra.fr/bioinfo/xtandempipeline.
.TP
.I The OBI-Warp alignment library
http://obi-warp.sourceforge.net/
.SH "LICENCE"
MassChroQ is licenced under the terms of the ?
For information on this licence look at the source code that came with
the software or see the ?
.SH "COPYRIGHT"
The copyright on masschroq and the source code is held by RIEN DU TOUT
.SH AUTHORS
.SS MassChroQ
Benoît Valot <valot@moulon.inra.fr>
.TP
Olivier Langella <langella@moulon.inra.fr>
.TP
Edlira Nano <nano@moulon.inra.fr>
.TP
Michel Zivy <zivy@moulon.inra.fr>
.SS This manual page
Edlira Nano <nano@moulon.inra.fr>
/usr/local/bin/masschroq
/usr/local/share/xml/schema/masschroq.xsd
/usr/local/share/man/man1/masschroq.1.gz
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