debian/0000755000000000000000000000000012171472555007177 5ustar debian/mmass-modules.30000644000000000000000000000267512171472555012063 0ustar .TH "MMASS" "3" "2010/03/12" "" "" .SH "NAME" mmass\-modules \- a free mass spectrometry tool for proteomics \(em C-based extension modules .SH "SYNOPSIS" .HP 7 \fBmmass\-modules\fR .SH "DESCRIPTION" .PP This manual page briefly documents the \fBmmass\-modules\fR package, a package that ships C-language extensions to the \fBmmass\fR package. .PP The \fBmmass\-modules\fR package currently ships only one extension, the \fIcalculations.so\fR extensions that is used to perform high performance calculations routines in the mass spectrum plotting module. .PP .SH "SEE ALSO" .PP mmass (1), mmass-doc(7). .PP .RE .SH "AUTHORS" .PP \fBMartin Strohalm\fR <\&support@mmass\&.org\&> .sp -1n .IP "" 4 Program author (contact him via http://www.mmass.org website's form)\&. .PP \fBFilippo Rusconi\fR <\&rusconi\&-debian\&@laposte\&.net\&> .sp -1n .IP "" 4 Man\-page author for the Debian distribution\&. .SH "COPYRIGHT" Copyright \(co 2005-2010 Martin Strohalm .br Copyright \(co 2011 Filippo Rusconi .br .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'. debian/start-script0000644000000000000000000000017112171472555011560 0ustar #!/bin/sh export PYTHONPATH=/usr/lib/mmass/mspy/${PYTHONPATH:+:$PYTHONPATH} exec python /usr/share/mmass/mmass.py "$@" debian/mmass-modules.lintian-overrides0000644000000000000000000000006312171472555015344 0ustar no-upstream-changelog hardening-no-stackprotector debian/mmass.10000644000000000000000000000405612171472555010406 0ustar .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 "BIBLIOGRAPHICAL REFERENCES TO BE CITED" .PP Strohalm M, Kavan D, Novak P, Volny M, Havlicek V: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data. Anal Chem 82 (11), 4648-51 (2010). DOI:10.1021/ac100818g .PP Strohalm M, Hassman M, Košata B, Kodíček M: mMass data miner: an open source alternative for mass spectrometric data analysis. Rapid Commun Mass Spec 22 (6), 905-908 (2008). DOI:10.1002/rcm.3444 .PP .SH "SEE ALSO" .PP mmass-modules (3), mmass-doc(7). .PP .RE .SH "AUTHORS" \fBMartin Strohalm\fR <\&support@mmass\&.org\&> .sp -1n .IP "" 4 Program author (contact him via http://www.mmass.org website's form)\&. .PP \fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&> .sp -1n .IP "" 4 Man\-page author for the Debian distribution. .SH "COPYRIGHT" Copyright \(co 2005-2010 Martin Strohalm .br Copyright \(co 2010,2011 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'. debian/source/0000755000000000000000000000000012171472555010477 5ustar debian/source/format0000644000000000000000000000001512171472555011706 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000150212171472555011354 0ustar The software is shipped with precompiled binaries, in particular a shared object targeting the MacOSX platform and a pyd dll file for the MSWindows platform. These binaries have been removed during repackaging. All .pyc files have been removed. One build/ directory was removed also. The source zip file also contains set of graphics images (icons, for the most part) targeting MSWindows and MacOSX and Gtk. All the graphics files not in the Gtk directory were removed during repackaging. Almost all the files have the execution bit set ; this has been fixed during repackaging. Finally, the user manual, which comes as a PDF-formatted file, with no source and no license, is being removed also. See the rules:get-orig-source target for the details. -- Filippo Rusconi , Mon, 11 Apr 2011 22:19:59 +0200 debian/mmass-modules.install0000644000000000000000000000007412171472555013356 0ustar mspy/build/lib.*-*-2.*/calculations.so usr/lib/mmass/mspy debian/README.Debian0000644000000000000000000000114612171472555011242 0ustar mmass for Debian ================ The mmass software, based at http://www.mmass.org, allows one to integrate mass data about a number of biological molecules. These data are available from the Download page, section "mMass Databases". The Debian package of the mMass software cannot ship the User Guide that is provided by the upstream software author, because the source of that User Guide is not in a usable standard format. However, the User Guide is available at http://mmass.org/download/files/mmass_v3.10.0_user_guide.pdf. -- Filippo Rusconi , Mon, 11 Apr 2011 23:12:45 +0200 debian/mmass.install0000644000000000000000000000027212171472555011710 0ustar debian/mmass.desktop usr/share/applications debian/mmass.xpm usr/share/pixmaps configs usr/share/mmass mmass.py usr/share/mmass mspy/*.py usr/share/mmass/mspy gui usr/share/mmass debian/control0000644000000000000000000000364012171472555010605 0ustar Source: mmass Section: science Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi Build-Depends: debhelper (>= 7), dpkg-dev (>= 1.16.1~), python (>= 2.5), python-all, python-all-dev (>= 2.6.6-14), python-numpy (>= 1.4.1), imagemagick Standards-Version: 3.9.4 Homepage: http://www.mmass.org/ Vcs-Git: git://anonscm.debian.org/debichem/packages/mmass.git Vcs-Browser: http://anonscm.debian.org/git/debichem/packages/mmass.git #XS-Python-Version: >= 2.6 Package: mmass Architecture: all Depends: ${misc:Depends}, ${python:Depends}, python-wxgtk2.8 (>= 2.8.10.1-3+b1), python-numpy (>= 1.4.1), mmass-modules (>= ${binary:Version}) XB-Python-Version: ${python:Versions} 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. . The software can be easily extended by additional Python modules. This package contains the platform-independent parts of the software. Package: mmass-modules Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends} XB-Python-Version: ${python:Versions} Description: Mass spectrometry tool for proteomics - extension modules 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. . The software can be easily extended by additional Python modules. This package contains the platform-dependent parts of the software. debian/compat0000644000000000000000000000000212171472555010375 0ustar 7 debian/mmass.dirs0000644000000000000000000000005712171472555011204 0ustar usr/bin usr/share/mmass usr/share/mmass/mspy debian/upstream0000644000000000000000000000064412171472555010766 0ustar Reference: Author: Martin Strohalm Title: A cross-platform software environment for precise analysis of mass spectrometric data Journal: Analytical chemistry (ACS) Year: 2010 Volume: 82 Number: 11 Pages: 4648-4651 DOI: 10.1021/ac100818g PMID: 20465224 URL: http://pubs.acs.org/doi/abs/10.1021/ac100818g eprint: http://pubs.acs.org/doi/pdf/10.1021/ac100818g Repository : http://mmass.org/download/ debian/mmass.manpages0000644000000000000000000000002012171472555012024 0ustar debian/mmass.1 debian/mmass.desktop0000644000000000000000000000035512171472555011715 0ustar [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;Biology;Chemistry Keywords=Mass spectrometry;Data analysisdebian/mmass.lintian-overrides0000644000000000000000000000002712171472555013676 0ustar no-upstream-changelog debian/mmass.menu0000644000000000000000000000024212171472555011203 0ustar ?package(mmass):\ needs="X11"\ section="Applications/Science/Chemistry"\ title="mMass"\ icon="/usr/share/pixmaps/mmass.xpm" \ command="/usr/bin/mmass" debian/mmass.docs0000644000000000000000000000001412171472555011164 0ustar readme.txt debian/copyright0000644000000000000000000000512212171472555011132 0ustar 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, 2008, 2009, 2010, 2011 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 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. 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. 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 (file LICENSE.TXT) for more details. 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-3'. The original upstream source tarball contained a large amount of unacceptable files. The preparation of a suitable orig.tar.gz file was performed using the following commands from inside the development tree, in the top source directory: see rules:get-orig-source target for the details. The Debian packaging is © 2009, 2010, 2011 Filippo Rusconi and is licensed under the GPL-3+, see `/usr/share/common-licenses/GPL-3'. debian/rules0000755000000000000000000000571412171472555010266 0ustar #!/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 VERSION="4.0.0" PYVERS=$(shell pyversions -r) INSTALLDIR=$(CURDIR)/debian/$(PACKAGE) DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk # Using the flag below confirms the protection works fine. # But we need not use it. Cf Debian wiki. # Thus setting a lintian override. # CFLAGS += -fstack-protector-all ######################### clean ######################### .PHONY: clean clean: dh_testdir dh_testroot rm -f debian/mmass.xpm rm -rf $(INSTALLDIR) rm -rf mspy/plot/build dh_clean ######################### build ######################### build-arch-stamp: dh_testdir dh_prep -a convert gui/images/gtk/icon_32.png debian/mmass.xpm # This will create the "calculations.so" shared object in # mspy/plot/build/lib.linux-i686-2.6. This shared object will # have to be installed as # /usr/lib/mmass/mspy/plot/calculations.so. Note that because # the build path changes according to the platform, the # mmass.install file has a '*' wildcard in the directory name. cd mspy && python setup.py build touch build-arch-stamp .PHONY: build-indep build-indep: .PHONY: build-arch build-arch: build-arch-stamp .PHONY: build build: build-indep build-arch ######################### binary ######################### .PHONY: binary-arch binary-arch: build-arch dh_testdir -a dh_testroot -a dh_installdirs -a dh_lintian -a dh_installchangelogs -a dh_installdocs -a dh_install -a dh_installmenu -a dh_python2 -a dh_installman -a dh_compress -a dh_shlibdeps -a dh_fixperms -a dh_strip -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a .PHONY: binary-indep binary-indep: dh_testdir -i dh_testroot -i dh_prep -i dh_installdirs -i dh_lintian -i cp debian/start-script $(INSTALLDIR)/usr/bin/mmass -i dh_installchangelogs -i dh_installdocs -i dh_install -i dh_installman -i dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i .PHONY: binary binary: binary-indep binary-arch get-orig-source: wget http://mmass.org/download/files/mmass_v$(VERSION)_source.zip unzip mmass_v$(VERSION)_source.zip rm -r mmass_v$(VERSION)_source.zip mv mMass mmass-upstream-$(VERSION).orig find mmass-upstream-$(VERSION).orig -name "mmass.tmproj" -delete find mmass-upstream-$(VERSION).orig -name "*.pyc" -delete find mmass-upstream-$(VERSION).orig -name "*.pyd" -delete find mmass-upstream-$(VERSION).orig -name "*.so" -delete rm "mmass-upstream-$(VERSION).orig/User Guide.pdf" rm -rf mmass-upstream-$(VERSION).orig/mspy/plot/build find mmass-upstream-$(VERSION).orig -type f -executable -exec chmod a-x '{}' \; rm -rf mmass-upstream-$(VERSION).orig/gui/images/mac/ rm -rf mmass-upstream-$(VERSION).orig/gui/images/msw/ tar cf - mmass-upstream-$(VERSION).orig | gzip --best > mmass_$(VERSION).orig.tar.gz rm -rf mmass-upstream-$(VERSION).orig debian/watch0000644000000000000000000000012712171472555010230 0ustar version=3 http://www.mmass.org/download \ files/v[\d\.]*/mmass_v([\d\.]*)_source.zip debian/changelog0000644000000000000000000002077712171472555011066 0ustar mmass (5.5.0-2) unstable; urgency=low * debian/watch: fix syntax error. Thanks to Daniel Leidert for reporting the bug (Closes: #675840) and to Sebastian Gibb for pinging me about it. -- Filippo Rusconi Wed, 17 Jul 2013 12:41:52 +0200 mmass (5.5.0-1) unstable; urgency=low * New upstream release; * debian/mmass.desktop: add Keywords field; * debian/control: canonicalized the Vcs* fields; -- Filippo Rusconi Wed, 03 Jul 2013 10:30:03 +0200 mmass (5.4.1-1) unstable; urgency=low * New upstream release. -- Filippo Rusconi Thu, 17 Jan 2013 11:28:55 +0100 mmass (5.4.0-1) unstable; urgency=low * New upstream release. -- Filippo Rusconi Sun, 18 Nov 2012 23:11:24 +0100 mmass (5.3.0-1) unstable; urgency=low * New upstream release. * Fix problem with absent build dependency [dpkg-dev (>= 1.16.1~)]. -- Filippo Rusconi Thu, 13 Sep 2012 14:11:45 +0200 mmass (5.2.0-2) unstable; urgency=low * Fix bug in the debian/start-script that did not pass the command line arguments to the mmass.py program. -- Filippo Rusconi Mon, 23 Jul 2012 14:23:47 +0200 mmass (5.2.0-1) unstable; urgency=low * New upstream release. -- Filippo Rusconi Mon, 02 Jul 2012 22:43:45 +0200 mmass (5.1.0-1) unstable; urgency=low * New upstream release implementing, amongst others, a suggestion that I made to Martin Strohalm : to compute the mass of the analyte and display it right away on the basis of the span tool that might be gragged between to consecutive peaks in an isotopic cluster. * Add hardening build flags in debian/rules to fix the hardening-no-stackprotector lintian warning about building the mspy/calculations.so module. * Add debian/upstream file to document a scientific article describing mmass. * Add lintian overrides for mmass and mmass-modules. -- Filippo Rusconi Thu, 24 May 2012 12:01:23 +0200 mmass (5.0.1-1) unstable; urgency=low * New upstream release (bug fixes). -- Filippo Rusconi Fri, 20 Apr 2012 17:25:50 +0200 mmass (5.0.0-1) unstable; urgency=low * New upstream release. - Updated debian/* files as the mspy/plot directory has gone and this is where the calculations.c code file was compile. -- Filippo Rusconi Wed, 21 Mar 2012 22:40:05 +0100 mmass (4.0.0-1) unstable; urgency=low * New upstream release. - Feature improvements. One of these was suggested by me: provide automatically the charge of the ion that produced one isotopic peak over which the space ruler is used. -- Filippo Rusconi Wed, 07 Dec 2011 22:04:02 +0100 mmass (3.12.1-1) unstable; urgency=low * New upstream release. - Bug fixes. One of the bugs was reported by me : crash when closing last document. -- Filippo Rusconi Mon, 29 Aug 2011 09:37:13 +0200 mmass (3.12.0-1) UNRELEASED; urgency=low * New upstream release. - Found a bug and reported it. Not releasing, waiting for new version. -- Filippo Rusconi Sun, 28 Aug 2011 16:55:32 +0200 mmmmass (3.11.0-3) unstable; urgency=low * Move to dh_python2 pacakging helper; * Change my address to lopippo@debian.org and remove the DM-Upload-Allowed field. -- Filippo Rusconi Fri, 01 Jul 2011 21:13:45 +0200 mmass (3.11.0-2) unstable; urgency=low * Change calculations.so install path so that the kFreeBSD kernel is supported along with Linux (Closes: #626743). Thanks to Christoph Egger for reporting the bug and providing the patch to fix it. -- Filippo Rusconi Sun, 15 May 2011 10:56:37 +0200 mmass (3.11.0-1) unstable; urgency=low * New upstream release; * rules: fix clean target : remove the rm -f debian/mmass.pdf command, as the user guide is no more shipped within the mmass package (DFSG); * rules: update the VERSION number and also improve the get-orig-source target removing one more lint file from the source tarball. -- Filippo Rusconi Thu, 12 May 2011 18:06:54 +0200 mmass (3.10.0-1) unstable; urgency=low * New upstream release. * Fix restrictive dependency on python2.6 (Closes: #617758). Now python2.x is allowed. Following suggestion by Fabrice Coutadeur (thanks for the patch). * Put the calculations.so private extension into a new mmass-modules binary package. Remove the corresponding lintian override. * Make a clear statement of how the upstream source tarball was repackaged to yield the orig.tar.gz file. The description is located at the bottom of the copyright file and in the README.Debian-source file. * Remove the mmass-doc binary package to ship the user guide PDF-formatted file as it comes in upstream's source tarball with no source and no license (remove dependency on mmass-doc for binary package mmass); * Update copyright date and legal text to reflect the wording in the new version; * debian/copyright : fix one typo in the GPL version (Thanks Joachim Reichel ); * Rename README.Debian-source to README.source (Thanks Joachim Reichel ); * debian/rules: add get-orig-source target (Thanks Joachim Reichel ); * Add README.Debian to document the absence of the User Guide. Get installed via mmass.docs (Thanks Joachim Reichel ); * Reworded the description of the binary pacakged in the control file (Thanks Joachim Reichel ); * Sponsored upload by Joachim Reichel ; -- Filippo Rusconi Tue, 12 Apr 2011 13:47:11 +0200 mmass (3.9.0-1) unstable; urgency=low * New upstream release. -- Filippo Rusconi Fri, 14 Jan 2011 22:59:02 +0100 mmass (3.8.0-2) unstable; urgency=low * debian/start-script: fix insecure PYTHONPATH setting by making sure the variable is not empty (thanks Jakub Wilk for pointing to the problem and to Chow Loong Jin and Vincent Bernat for the suggested fix). -- Filippo Rusconi Fri, 26 Nov 2010 14:01:21 +0100 mmass (3.8.0-1) unstable; urgency=low * New upstream release (Closes: #600752). This packaging has been reworked as the upstream software was entirely rewritten. The package now includes code to build a private module. The user manual is no more a set of HTML files but one single PDF file. Packaging was thusly adapted. Note that a new mmass-modules package was initially envisaged, but since we are in release times in the new package would force a sieve through the NEW queue, we sticked to a single binary 'any' package containing arch-dep and arch-indep stuff. Thanks to DD Michael Banck for the suggestion. * Set source format to 3.0 (quilt). -- Filippo Rusconi Mon, 01 Nov 2010 15:17:10 +0100 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 debian/mmass-modules.manpages0000644000000000000000000000003012171472555013473 0ustar debian/mmass-modules.3