--- mmass-2.4.0.orig/debian/mmass.install +++ mmass-2.4.0/debian/mmass.install @@ -0,0 +1,11 @@ +debian/mmass.desktop usr/share/applications +debian/mmass.xpm usr/share/pixmaps + +images/*.png usr/share/mmass/images + +configs usr/share/mmass + +mmass.py usr/share/mmass + +nucleus usr/share/mmass +modules usr/share/mmass --- mmass-2.4.0.orig/debian/mmass.manpages +++ mmass-2.4.0/debian/mmass.manpages @@ -0,0 +1,2 @@ +debian/mmass.1 + --- mmass-2.4.0.orig/debian/changelog +++ mmass-2.4.0/debian/changelog @@ -0,0 +1,39 @@ +mmass (2.4.0-4) unstable; urgency=low + + * debian/control: add ${misc:Depends} dependency to Depends: field (so + as to remove one lintian warning); + * debian/control: bump up Standards-Version: 3.8.3. + + -- Filippo Rusconi Wed, 13 Jan 2010 17:51:56 +0100 + +mmass (2.4.0-3) unstable; urgency=low + + * debian/changelog: add field XS-Python-Version: >= 2.4 and make + Depends: ${python:Depends} instead of Depends: python2.5 | python2.4; + + * debian/start-script: remove conditional on the presence of python2.4 + or python2.5, start program with exec python + /usr/share/mmass/mmass.py; + + * Both changes above are to prepare for introduction of Python2.6 and + removal of Python2.5 (Closes: #561162). Thanks to Jakub Wilk + for the patch. + + -- Filippo Rusconi Tue, 15 Dec 2009 22:20:37 +0100 + +mmass (2.4.0-2) unstable; urgency=low + + * watch: fix rule to match new mmass.org site and structure. + + * Fixes in the man pages; + + * Add -i do dh_* in binary-indep target. + + -- Filippo Rusconi Fri, 06 Nov 2009 09:29:03 +0100 + +mmass (2.4.0-1) unstable; urgency=low + + * Initial release (Closes: #525675); + + -- Filippo Rusconi Wed, 20 May 2009 23:30:28 +0200 + --- mmass-2.4.0.orig/debian/mmass.1 +++ mmass-2.4.0/debian/mmass.1 @@ -0,0 +1,53 @@ +.TH "MMASS" "1" "November 2009" + +.SH "NAME" +mmass \- a free mass spectrometry tool for proteomics + +.SH "SYNOPSIS" +\fBmmass\fR + +.SH "DESCRIPTION" +\fBmmass\fR is a free mass spectrometry tool for proteomics. Its main +feature is its capability to load mass spectral data in its powerful +mass spectrum viewer. The program can load data in the following +formats: mzData, mzXML, raw text. The mass spectrum viewer allows +performing a large number of operations commonly required when +analyzing mass spectrometry data (zoom, pan, rapid delta-mass +calculations, peak picking and so forth). The program will allow +defining peak lists, recalibrating spectra, performing some +protein-only simulations and doing on-line Mascot searches. + +.SH "EXAMPLE DATA" +Example data are located in \fI\%/usr/share/doc/mmass/examples\fP. + +.SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" +.PP +Strohalm M, Hassman M, Kosata B, Kodicek M: mMass data miner: an open +source alternative for mass spectrometric data analysis. Rapid +Commun. Mass Spec. (2008) 22, 6, 905 - 908. + +.SH "AUTHORS" +\fBMartin Strohalm\fR <\&mmass@biographics.cz\&> +.sp -1n +.IP "" 4 +Program author. +.PP +\fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&> +.sp -1n +.IP "" 4 +Man\-page author for the Debian distribution. + +.SH "COPYRIGHT" +Copyright \(co 2005-2007 Martin Strohalm +.br +Copyright \(co 2009 Filippo Rusconi +.PP +This manual page was written by Filippo Rusconi +<\&rusconi\-debian@laposte.net\&> for the Debian system (but may be +used by others). Permission is granted to copy, distribute and/or +modify this document under the terms of the GNU General Public +License, Version 3, published by the Free Software Foundation. +.PP + On a Debian system the complete text of the GNU General Public +License version 3 can be found in the file +`\fI\%/usr/share/common-licenses/GPL\-3\fP'. --- mmass-2.4.0.orig/debian/start-script +++ mmass-2.4.0/debian/start-script @@ -0,0 +1,4 @@ +#!/bin/sh + +exec python /usr/share/mmass/mmass.py + --- mmass-2.4.0.orig/debian/mmass-doc.7 +++ mmass-2.4.0/debian/mmass-doc.7 @@ -0,0 +1,40 @@ +.TH "MMASS" "7" "2009/04/25" "" "" +.SH "NAME" +mmass\-doc \- a free mass spectrometry tool for proteomics \(em documentation +.SH "SYNOPSIS" +.HP 7 +\fBmmass\-doc\fR +.SH "DESCRIPTION" +.PP + +This manual page briefly documents the \fBmmass\-doc\fR package, the +user manual for \fBmmass\fR\& in HTML format located at +/usr/share/doc/mmass-doc. It can also be read online at +http://mmass.biographics.cz/en/documentation. +.PP +.SH "SEE ALSO" +.PP +mmass (1). +.PP +.RE +.SH "AUTHORS" +.PP +\fBMartin Strohalm\fR <\&mmass@biographics\&.cz\&> +.sp -1n +.IP "" 4 +Program author\&. +.PP +\fBFilippo Rusconi\fR <\&rusconi\&-debian\&@laposte\&.net\&> +.sp -1n +.IP "" 4 +Man\-page author for the Debian distribution\&. +.SH "COPYRIGHT" +Copyright \(co 2005-2007 Martin Strohalm +.br +Copyright \(co 2009 Filippo Rusconi +.br +.PP +This manual page was written for the Debian system (but may be used by others)\&. +.PP +Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation\&. +.sp --- mmass-2.4.0.orig/debian/mmass-doc.manpages +++ mmass-2.4.0/debian/mmass-doc.manpages @@ -0,0 +1,2 @@ +debian/mmass-doc.7 + --- mmass-2.4.0.orig/debian/mmass.dirs +++ mmass-2.4.0/debian/mmass.dirs @@ -0,0 +1,3 @@ +usr/bin +usr/share/mmass + --- mmass-2.4.0.orig/debian/mmass.desktop +++ mmass-2.4.0/debian/mmass.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Version=1.0 +Name=mMass +Comment=Mass spectrum viewer and data analysis proteomics tool +Type=Application +Exec=/usr/bin/mmass +Icon=mmass +Categories=Education;Science;Chemistry; --- mmass-2.4.0.orig/debian/mmass-doc.doc-base +++ mmass-2.4.0/debian/mmass-doc.doc-base @@ -0,0 +1,11 @@ +Document: mmass-documentation +Title: mMass +Author: Martin Strohalm +Abstract: This manual describes what mMass is and how it can be used + to view/analyze mass spectra and perform analyses related to + proteomics projects. +Section: Science/Chemistry + +Format: HTML +Index: /usr/share/doc/mmass-doc/doc/index.html +Files: /usr/share/doc/mmass-doc/doc --- mmass-2.4.0.orig/debian/control +++ mmass-2.4.0/debian/control @@ -0,0 +1,51 @@ +Source: mmass +Section: science +Priority: optional +Maintainer: The Debichem Group +Uploaders: Filippo Rusconi +DM-Upload-Allowed: yes +Build-Depends: debhelper (>= 7) +Build-Depends-Indep: python-support, imagemagick +Standards-Version: 3.8.3 +Homepage: http://www.mmass.org/ +Vcs-Git: git://git.debian.org/git/debichem/packages/mmass.git +Vcs-Browser: http://git.debian.org/?p=debichem/packages/mmass.git +XS-Python-Version: >= 2.4 + + +Package: mmass +Architecture: all +Depends: ${misc:Depends}, ${python:Depends}, python-wxgtk2.6 (>= 2.6.3.2), python-numpy (>= 1.0.1) +Suggests: mmass-doc +Description: Mass spectrometry tool for proteomics + mMass is a free mass spectrum viewer/analyzer in which the + following proteomics-related tasks can be performed: + . + - Open raw text, mzXML and mzData mass spectra; + - Define peak lists; + - Powerful mass spectrum viewer (zoom, cursor...); + - Data recalibration; + - Protein-only simulations; + - Online Mascot searches. + . + This software is written with Python, and the author claims that + writing new modules should be easy. + + +Package: mmass-doc +Section: doc +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Mass spectrometry tool for proteomics - documentation + mMass is a free mass spectrum viewer/analyzer in which the + following proteomics-related tasks can be performed: + . + - Open raw text, mzXML and mzData mass spectra; + - Define peak lists; + - Powerful mass spectrum viewer (zoom, cursor...); + - Data recalibration; + - Protein-only simulations; + - Online Mascot searches. + . + This package contains the user documentation in HTML format. + --- mmass-2.4.0.orig/debian/mmass-doc.install +++ mmass-2.4.0/debian/mmass-doc.install @@ -0,0 +1,2 @@ +doc/ usr/share/doc/mmass-doc + --- mmass-2.4.0.orig/debian/mmass.examples +++ mmass-2.4.0/debian/mmass.examples @@ -0,0 +1,2 @@ +examples/* + --- mmass-2.4.0.orig/debian/watch +++ mmass-2.4.0/debian/watch @@ -0,0 +1,5 @@ +version=3 + +http://www.mmass.org/download \ +files/mmass_v([\d\.]*)_source.tar.gz + --- mmass-2.4.0.orig/debian/mmass.menu +++ mmass-2.4.0/debian/mmass.menu @@ -0,0 +1,7 @@ +?package(mmass):\ + needs="X11"\ + section="Applications/Science/Chemistry"\ + title="mMass"\ + icon="/usr/share/pixmaps/mmass.xpm" \ + command="/usr/bin/mmass" + --- mmass-2.4.0.orig/debian/mmass.docs +++ mmass-2.4.0/debian/mmass.docs @@ -0,0 +1,3 @@ +history.txt +readme.txt + --- mmass-2.4.0.orig/debian/compat +++ mmass-2.4.0/debian/compat @@ -0,0 +1 @@ +7 --- mmass-2.4.0.orig/debian/copyright +++ mmass-2.4.0/debian/copyright @@ -0,0 +1,50 @@ +This work was packaged for Debian by: + +Filippo Rusconi on Sat, 25 Apr 2009 +14:45:01 +0200. + +It was downloaded from http://www.mmass.org/ + +Author: Martin Strohalm + +mMass Copyright © 2005, 2006, 2007 Martin Strohalm + +License for mmass: GNU General Public License. + + 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 2 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. + + The author insists that the users do actually read the license + entirely and understand it fully. He goes on: + + ---> "Please note in particular that, if you use this program, or + ANY part of it - even a single line of code - in another + application, the resulting application becomes also GPL. In other + words, GPL is a "contaminating" license. + + If you do not understand any portion of this notice, please seek + appropriate professional legal advice. If you do not or - for any + reason - you can not accept ALL of these conditions, then you must + not use nor distribute this program. + + The origin of this software must not be misrepresented; you must + not claim that you wrote the original software. Altered source + versions must be clearly marked as such, and must not be + misrepresented as being the original software. + + This notice must not be removed or altered from any source + distribution." <--- + + On Debian systems, the GNU General Public License, is available as + the file `/usr/share/common-licenses/GPL-2'. + +The Debian packaging is © 2009, Filippo Rusconi + and is licensed under the GPL-3+, see +`/usr/share/common-licenses/GPL-3'. --- mmass-2.4.0.orig/debian/rules +++ mmass-2.4.0/debian/rules @@ -0,0 +1,70 @@ +#!/usr/bin/make -f +# Based on the initial work of Joey Hess and Craig Small. + + +# Uncomment this to turn on verbose mode. +export DH_VERBOSE=1 + +PACKAGE=mmass + +INSTALLDIR=$(CURDIR)/debian/$(PACKAGE) + + +.PHONY: clean +clean: + dh_testdir + dh_testroot + dh_clean + + rm -f debian/mmass.xpm + + rm -rf $(INSTALLDIR) + +build-indep-stamp: + dh_testdir + dh_prep -i + + convert images/icon_win_32.png debian/mmass.xpm + + touch build-indep-stamp + +.PHONY: build-indep +build-indep: build-indep-stamp + +.PHONY: build-arch +build-arch: + +.PHONY: build +build: build-indep build-arch + +# Build architecture-independent files here. +.PHONY: binary-indep +binary-indep: build-indep + dh_testdir -i + dh_testroot -i + dh_prep -i + dh_installdirs -i + cp debian/start-script $(INSTALLDIR)/usr/bin/mmass -i + dh_installchangelogs -i + dh_installdocs -i + dh_installexamples -i + dh_install -i + dh_installmenu -i + dh_pysupport -i + dh_installman -i + dh_compress -i + dh_fixperms -i + dh_installdeb -i + dh_gencontrol -i + dh_md5sums -i + dh_builddeb -i + + +# Build architecture-dependent files here. +.PHONY: binary-arch +binary-arch: +# We have nothing to do: no arch-dependent package" + + +.PHONY: binary +binary: binary-indep binary-arch