debian/0000755000000000000000000000000012243622232007164 5ustar debian/tandem.10000644000000000000000000000363312243622232010523 0ustar .TH "TANDEM" "1" "November 2012" .SH "NAME" tandem \- X!Tandem mass spectrometry software for peptide sequencing .SH "SYNOPSIS" \fBtandem\fR .SH "DESCRIPTION" This manual page documents briefly the \fBtandem-mass\fR package that brings a mass spectrometric software software for peptide sequencing and protein identification. This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at \fI`http://www.thegpm.org/docs/X_series_output_form.pdf'\fR. Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Robertson Craig and Ronald C. Beavis. (2004) TANDEM: matching proteins with mass spectra. \fIBioinformatics\fP, 20, 1466-1467. See more references pertaining to this software at `http://www.thegpm.org/GPM/references.html'. .SH "AUTHOR" This manual page was written by Filippo Rusconi <\&lopippo@debian.org\&>. 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/0000755000000000000000000000000012243622232010464 5ustar debian/source/format0000644000000000000000000000001512243622232011673 0ustar 3.0 (quilt) debian/control0000644000000000000000000000325412243622232010573 0ustar Source: tandem-mass Section: science Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi Standards-Version: 3.9.4 Build-Depends: debhelper (>= 7.0.50~), dpkg-dev (>= 1.16.1~), libexpat1-dev (>= 2.0.1) Homepage: http://www.thegpm.org/TANDEM/ Vcs-Git: git://anonscm.debian.org/debichem/packages/tandem-mass.git Vcs-Browser: http://anonscm.debian.org/git/debichem/packages/tandem-mass.git Package: tandem-mass Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: mass spectrometry software for protein identification X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification. . This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at \fI`http://www.thegpm.org/docs/X_series_output_form.pdf'\fR. . Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. debian/compat0000644000000000000000000000000212243622232010362 0ustar 7 debian/upstream0000644000000000000000000000075512243622232010756 0ustar Reference: Author: Peter Bowden and Ron Beavis and John Marshall Title: Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system. Journal: Journal of proteomics Year: 2009 Volume: 73 Number: 1 Pages: 103-111 DOI: 10.1016/j.jprot.2009.08.004 PMID: 19703602 URL: http://www.sciencedirect.com/science/article/pii/S1874391909002437 eprint: debian/patches/0000755000000000000000000000000012243622232010613 5ustar debian/patches/series0000644000000000000000000000005512243622232012030 0ustar debian-makefile fix-missing-include-string-h debian/patches/debian-makefile0000644000000000000000000000114012243622232013527 0ustar Fix the makefile to suit Debian building --- a/src/Makefile_ubuntu +++ b/src/Makefile_ubuntu @@ -1,8 +1,8 @@ #makefile for c++ programs #change the name of the executable to use for "any" project -EXECUTABLE = ../bin/tandem.exe -#EXECUTABLE = ../bin/p3.exe +EXECUTABLE = ../bin/tandem +#EXECUTABLE = ../bin/p3 LINKCC = $(CXX) #CXXFLAGS denotes flags for the C++ compiler @@ -11,8 +11,8 @@ #uncomment this line if you are using gcc 4.x -CXXFLAGS = -w -O2 -DGCC4_3 -#CXXFLAGS = -w -O2 -DGCC4_3 -DX_P3 +#CXXFLAGS = -w -O2 -DGCC4_3 +CXXFLAGS = -w -O2 #ubuntu 64 bit version debian/patches/fix-missing-include-string-h0000644000000000000000000000272612243622232016154 0ustar Fix missing #înclude --- a/src/base64.cpp +++ b/src/base64.cpp @@ -5,6 +5,7 @@ #include "stdafx.h" #include "base64.h" +#include "string.h" inline int getPosition( char buf ); --- a/src/saxhandler.h +++ b/src/saxhandler.h @@ -135,6 +135,7 @@ #include // strcpm #include #include "mspectrum.h" +#include "string.h" /** * eXpat SAX parser wrapper. --- a/src/mhistogram.h +++ b/src/mhistogram.h @@ -131,6 +131,8 @@ #ifndef MHISTOGRAM_H #define MHISTOGRAM_H +#include "string.h" + // File version: 2003-07-01 /* --- a/src/mcleave.h +++ b/src/mcleave.h @@ -131,6 +131,8 @@ #ifndef MCLEAVE_H #define MCLEAVE_H +#include "string.h" + // File version: 2006-03-10 /* * mcleave is a specialty class meant to store information about protein cleavage specificity --- a/src/mmotif.h +++ b/src/mmotif.h @@ -131,6 +131,8 @@ #ifndef MMOTIF_H #define MMOTIF_H +#include "string.h" + // File version: 2004-06-01 // File version: 2005-01-01 /* --- a/src/msequenceserver.cpp +++ b/src/msequenceserver.cpp @@ -145,6 +145,7 @@ #include "msequenceserver.h" #include "xmltaxonomy.h" #include +#include "string.h" msequenceServer::msequenceServer(void) { --- a/src/p3msequenceserver.cpp +++ b/src/p3msequenceserver.cpp @@ -145,6 +145,7 @@ #include "msequenceserver.h" #include "xmltaxonomy.h" #include +#include "string.h" p3msequenceServer::p3msequenceServer(void) { debian/tandem-mass.lintian-overrides0000644000000000000000000000010312243622232014747 0ustar no-upstream-changelog spelling-error-in-binary hardening-no-relro debian/tandem-mass.manpages0000644000000000000000000000002012243622232013102 0ustar debian/tandem.1 debian/tandem-mass.install0000644000000000000000000000003012243622232012756 0ustar bin/tandem usr/bin debian/tandem-mass.dirs0000644000000000000000000000001012243622232012247 0ustar usr/bin debian/copyright0000644000000000000000000000313412243622232011120 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ X-Debianized-By: Olivier Langella X-Debianized-Date: Thu, 15 Jan 2009 11:18:51 +0200 X-Source-Downloaded-From: http://www.thegpm.org/TANDEM/ X-Upstream-Author: Copyright © 2004, The Global Proteome Machine Organization Files: * Copyright: © 2004, The Global Proteome Machine Organization License: Artistic License 1.0 The Artistic License for all X! software, binaries and documentation . On Debian systems, the full text of the Artistic License version 1.0 can be found in the file `/usr/share/common-licenses/Artistic'. Files: debian/* Copyright: © 2010 Olivier Langella 2012 Filippo Rusconi 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . 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'. debian/rules0000755000000000000000000000265012243622232010247 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 export DH_OPTIONS=-v # Hardening stuff, see http://wiki.debian.org/Hardening DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk CFLAGS+=$(CPPFLAGS) CXXFLAGS+=$(CPPFLAGS) # applying quilt the modern way (http://pkg-perl.alioth.debian.org/howto/quilt.html) %: dh $@ .PHONY: build build: build-stamp build-stamp: dh_testdir dh_prep # Proper Makefile settings have been defined in src/Makefile_ubuntu # with a corresponding patch. cd src && $(MAKE) -f Makefile_ubuntu touch build-stamp .PHONY: clean clean: dh_testdir dh_testroot dh_clean rm -f bin/tandem rm -f src/*.d src/*.o rm -f build-stamp .PHONY: build-indep build-indep: # We have nothing to do by default. .PHONY: build-arch build-arch: build # Build architecture-independent files here. .PHONY: binary-indep binary-indep: build-indep # We have nothing to do by default. # Build architecture-dependent files here. .PHONY: binary-arch binary-arch: build-arch dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installexamples dh_install dh_installman dh_lintian dh_strip dh_compress dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb .PHONY: binary binary: binary-indep binary-arch debian/watch0000644000000000000000000000026112243622232010214 0ustar version=3 opts="uversionmangle=s/^(\d+)-(\d+)-(\d+)-(\d+)/20$1\.$2.$3.$4/" \ ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-(\d{1,2}-\d{1,2}-\d{1,2}-\d).(zip|tar\.gz) debian/changelog0000644000000000000000000000421412243622232011037 0ustar tandem-mass (1:2013.09.01-1) unstable; urgency=low * Packaging of X!Tandem (SLEDGEHAMMER 2013.09.01, from http://www.thegpm.org/tandem/) for Debian GNU/Linux (Olivier Langella , with the great help of Filippo Rusconi ); * Upload by Filippo Rusconi . -- The Debichem Group Fri, 22 Nov 2013 10:21:32 +0200 tandem-mass (1:2013.06.15-1) unstable; urgency=low * quilt dependencies removed from rules. quilt is now used the modern way as decribed in http://pkg-perl.alioth.debian.org/howto/quilt.html * Packaging of X!Tandem (JACKHAMMER 2013.06.15, from http://www.thegpm.org/TANDEM/) for Debian GNU/Linux (Olivier Langella , with the great help of Filippo Rusconi ); * Upload by Filippo Rusconi ; -- The Debichem Group Thu, 29 Aug 2013 12:21:32 +0200 tandem-mass (1:2013.02.01.1-1) unstable; urgency=low * Packaging of X!Tandem (CYCLONE 2013.02.01.1, from http://www.thegpm.org/TANDEM/) for Debian GNU/Linux (Olivier Langella , with the great help of Filippo Rusconi ); * Added and tested debian/watch file (Filippo Rusconi); * Added debian/upstream file (Olivier Langella); -- Filippo Rusconi Fri, 07 Jun 2013 19:31:15 +0200 tandem-mass (20121001-2) unstable; urgency=low * Fix the target build-stamp by adding the $(QUILT_STAMPFN) dependency. This missing dependency seemingly caused problems in Ubuntu (as reported by Tim Gardner ; Closes: #695553). Thanks Tim. -- Filippo Rusconi Wed, 16 Jan 2013 21:26:08 +0100 tandem-mass (20121001-1) unstable; urgency=low * Initial packaging of X!Tandem (CYCLONE 12-10-01-1, from http://www.thegpm.org/TANDEM/) for Debian GNU/Linux (in collaboration with Olivier Langella ). (Closes: #693800). -- Filippo Rusconi Wed, 14 Nov 2012 14:46:19 +0100