debian/0000775000000000000000000000000012255352155007175 5ustar debian/libpwiz3.install0000664000000000000000000000022512254744107012330 0ustar debian/build/usr/lib/libpwiz.so.3.0.0 usr/lib # The example source code files. pwiz_tools/examples/*.cpp usr/share/doc/libpwiz3/example-files debian/libpwiz-dev.dirs0000664000000000000000000000002412254744066012315 0ustar usr/lib usr/include debian/msconvert.sgml0000664000000000000000000002127412254744107012110 0ustar 05 december 2013 MSCONVERT 1 msconvert msconvert Convert mass spectrometry data file formats. msconvert DESCRIPTION This manual page documents briefly the msconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry data files from one format to another. Since this version is built on the Free Software Debian platform, only conversions involving Free Software can be performed [that is, *not* involving proprietary Microsoft Windows-based dynamic linking libraries (dlls)]. OPTIONS -v | --verbose Display detailed processing progress information. --help Show this message, with extra detail on filter options. -f | --filelist filename Uses the contents of filename which lists filenames. -o | --outdir dir Set the output directory ('-' for stdout) to dir. By default, the output directory is '.' (that is, the current working directory). -c | --config filename Set the configuration file to filename. --outfile filename Override the name of the output file. -e | --ext ext Set the extension of the output files to ext. Can be mzML or mzXML or mgf or txt. --mzML Write mzML format (default). --mzXML Write mzXML format. --mgf Write mgf Mascot generic format. --text Write ProteoWizard internal text format. --ms1 Write MS1 format. --cms1 Write CMS1 format. --ms2 Write MS2 format. --cms2 Write CMS2 format. --64 Set default binary encoding to 64-bit precision (default). --32 Set default binary encoding to 32-bit precision. --mz64 Encode m/z values in 64-bit precision (default). --mz32 Encode m/z values in 32-bit precision. --inten64 Encode intensity values in 64-bit precision. --inten32 Encode intensity values in 32-bit precision (default). --noindex Do not write index. -i | --contactInfo filename Use filename for contact info. -z | --zlib Use zlib compression for binary data. -g | --gzip gzip entire output file (adds .gz to filename). --filter arg Add a spectrum list filter. --merge Create a single output file from multiple input files by merging file-level metadata and concatenating spectrum lists. --simAsSpectra Write selected ion monitoring as spectra, not chromatograms. --srmAsSpectra Write selected reaction monitoring as spectra, not chromatograms. EXAMPLES Convert data.RAW to data.mzXML msconvert data.RAW --mzXML Put output file in my_output_dir msconvert data.RAW -o my_output_dir Extract scan indices 5...10 and 20...25 msconvert data.RAW --filter "index [5,10] [20,25]" Extract MS1 scans only msconvert data.RAW --filter "msLevel 1" Extract MSn scans for n>1 msconvert data.RAW --filter "msLevel 2-" Use a configuration file msconvert data.RAW -c config.txt RETURN VALUE The number of failed files. AUTHOR Filippo Rusconi <lopippo@debian.org> This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). 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. On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL\-3'. debian/libpwiz-doc.dirs0000664000000000000000000000003712254744066012310 0ustar usr/share/doc/libpwiz-doc/dox debian/libpwiz3.links0000664000000000000000000000006412254744066012007 0ustar usr/lib/libpwiz.so.3.0.0 usr/lib/libpwiz.so.3 debian/libpwiz.30000664000000000000000000000657712254744066010765 0ustar .TH "LIBPWIZ" "3" "October 2012" .SH "NAME" libpwiz \- library to perform proteomics data analyses (runtime) .SH "DESCRIPTION" This manual page documents briefly the \fBlibpwiz\fR package that brings a library library to perform proteomics data analyses. ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. .SH "EXAMPLES OF BINARIES"-Ipwiz/data/msdata/ramp All these programs (in `/usr/lib/libpwizX/example-files' could be built using the command line shown after the binary name: \- mscat (g++ \-I /usr/include/libpwiz \-l pwiz mscat.cpp \-o mscat) .PP \- hello_analyzer_2 (g++ \-I /usr/include/libpwiz \-l pwiz hello_analyzer_2.cpp \-o hello_analyzer_2) .PP \- hello_analyzer (g++ \-I /usr/include/libpwiz \-l pwiz hello_analyzer.cpp \-o hello_analyzer) .PP \- hello_msdata (g++ \-I /usr/include/libpwiz \-l pwiz hello_msdata.cpp \-o hello_msdata) .PP \- txt2mzml (g++ \-I /usr/include/libpwiz \-l pwiz \-l boost_filesystem \-l boost_system txt2mzml.cpp \-o txt2mzml) .PP \- hello_ramp (g++ \-I /usr/include/libpwiz \-I /usr/include/libpwiz/pwiz/data/msdata/ramp \-l pwiz hello_ramp.cpp \-o hello_ramp) .PP \- write_example_files (g++ \-I /usr/include/libpwiz \-l pwiz write_example_files.cpp \-o write_example_files) .PP \- write_mzid_example_files (g++ \-I /usr/include/libpwiz \-l pwiz write_mzid_example_files.cpp \-o write_mzid_example_files) .PP \- write_proteome_example_files (g++ \-I /usr/include/libpwiz \-l pwiz write_proteome_example_files.cpp \-o write_proteome_example_files) .PP \- write_traml_example_files (g++ \-I /usr/include/libpwiz \-l pwiz write_traml_example_files.cpp \-o write_traml_example_files) .PP The \-I /usr/include/libpwiz specifies the location of the include files for the whole proteowizard project. The \-l pwiz specifies the libpwiz library to be linked\-in so as to build the binaries. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. (2012) A cross-platform toolkit for mass spectrometry and proteomics. \fI Nature Biotechnology\fP, 30. 10.1038/nbt.2377. .SH "SEE ALSO" .BR libpwiz\-dev (3), .BR libpwiz\-doc (7), .PP The library is documented fully in the doxygen-extacted documentation that is packaged in \fBlibpwiz\-doc\fR. .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/libpwiz-dev.lintian-overrides0000664000000000000000000000002712254744066015015 0ustar no-upstream-changelog debian/libpwiz-tools.manpages0000664000000000000000000000010712254744107013527 0ustar debian/msconvert.1 debian/idconvert.1 debian/mscat.1 debian/txt2mzml.1 debian/upstream0000664000000000000000000000151112254744066010763 0ustar Reference: Author: Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. Title: A cross-platform toolkit for mass spectrometry and proteomics. Journal: Nature Biotechnology Year: 2012 Volume: 30 Number: Pages: 918-920 DOI: 10.1038/nbt.2377 PMID: 23051804 Repository: http://proteowizard.sourceforge.net/downloads.shtml debian/libpwiz-tools.dirs0000664000000000000000000000001112254744107012667 0ustar usr/bin debian/copyright0000664000000000000000000002661612254744066011150 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: libpwiz Source: http://proteowizard.sourceforge.net/downloads.shtml Files: pwiz/* Copyright: 2005-2008 Spielberg Family Center for Applied Proteomics, Cedars Sinai Medical Center, Los Angeles, California 90048 License: Apache License Version 2.0 Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Files: pwiz/utility/misc/random_access_compressed_ifstream.cpp Copyright: 2008,2011 Insilicos LLC License: zlib.h This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Files: pwiz/utility/misc/mru_list.hpp Copyright: 2003-2008 Joaquin M Lopez Munoz License: Boost Software License - Version 1.0 Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: . The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Files: pwiz/utility/misc/SHA1.cpp Copyright: Dominik Reichl License: Public Domain 100% free public domain implementation of the SHA-1 algorithm by Dominik Reichl Web: http://www.dominik-reichl.de/ Files: pwiz/utility/math/MatrixInverse.hpp Copyright: http://www.crystalclearsoftware.com/cgi-bin/boost_wiki/wiki.pl?Effective_UBLAS/Matrix_Inversion License: Public Domain or Boost Software License - Version 1.0 Public domain or Boost Software License - Version 1.0 Files: pwiz_tools/* Copyright: Copyright 2008 Spielberg Family Center for Applied Proteomics, Cedars-Sinai Medical Center, Los Angeles, California 90048 License: Apache License, Version 2.0 See above Files: libraries/libsvm-3.0 Copyright: 2000-2010 Chih-Chung Chang and Chih-Jen Lin License: Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . 3. Neither name of copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: libraries/boost_aux/libs/thread/src/win32/tss_pe.cpp libraries/boost_aux/libs/libs/thread/src/win32/tss_pe-before_1_44.cpp Copyright: 2004 Aaron W. LaFramboise, Roland Schwarz, Michael Glassford 2007 Roland Schwarz, Anthony Williams, David Deakins License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/once.hpp Copyright: 2005-7 Anthony Williams 2005 John Maddock License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/thread_primitives.hpp Copyright: 2005-7 Anthony Williams 2007 David Deakins License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/tools/bcp/bcp.hpp libraries/boost_aux/tools/bcp/path_operations.cpp libraries/boost_aux/tools/bcp/output_licence_info.cpp libraries/boost_aux/tools/bcp/bcp_imp.[ch]pp libraries/boost_aux/tools/bcp/licence_info.[ch]pp libraries/boost_aux/tools/bcp/file_types.cpp libraries/boost_aux/tools/bcp/fileview.[ch]pp libraries/boost_aux/tools/bcp/main.cpp libraries/boost_aux/tools/bcp/copy_path.cpp libraries/boost_aux/tools/bcp/scan_licence.cpp libraries/boost_aux/tools/bcp/add_path.cpp Copyright: 2003 Dr John Maddock License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/tools/bcp/add_dependent_lib.cpp Copyright: 2009 Dr John Maddock License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/tools/bcp/scan_cvs_path.cpp Copyright: 2003-7 John Maddock 2007 Bjorn Roald License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/file_descriptor.hpp Copyright: 2008 CodeRage, LLC (turkanis at coderage dot com) 2003-2007 Jonathan Turkanis License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/iostreams/arbitrary_positional_facade.hpp libraries/boost_aux/boost/iostreams/filter/base64.hpp Copyright: 2006, 2007 Takeshi Mouri License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/memory_order.hpp Copyright: 2008, 2009 Peter Dimov License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/atomic.hpp Copyright: 2011 Helge Bahmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/enum* Copyright: 2005 Frank Laub License: Boost Software License - Version 1.0 See above. Files: libraries/boost_aux/boost/utility/* Copyright: 2007 Tobias Schwinger License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/lockfree/detail/tagged_ptr.hpp libraries/boost_aux/boost/lockfree/detail/tagged_ptr_dcas.hpp libraries/boost_aux/boost/lockfree/stack.hpp Copyright: 2008 Tim Blechmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/lockfree/detail/tagged_ptr_ptrcompression.hpp libraries/boost_aux/boost/lockfree/detail/freelist.hpp Copyright: 2008, 2009 Tim Blechmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/lockfree/detail/branch_hints.hpp Copyright: 2007, 2008 Tim Blechmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/lockfree/detail/prefix.hpp libraries/boost_aux/boost/lockfree/ringbuffer.hpp Copyright: 2009 Tim Blechmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/lockfree/detail/fifo.hpp Copyright: 2008, 2009, 2010 Tim Blechmann License: Boost Software License - Version 1.0 See above Files: libraries/boost_aux/boost/atomic/detail/valid_integral_types.hpp libraries/boost_aux/boost/atomic/detail/gcc-alpha.hpp libraries/boost_aux/boost/atomic/detail/integral-casts.hpp libraries/boost_aux/boost/atomic/detail/generic-cas.hpp libraries/boost_aux/boost/atomic/detail/gcc-x86.hpp libraries/boost_aux/boost/atomic/detail/base.hpp libraries/boost_aux/boost/atomic/detail/interlocked.hpp libraries/boost_aux/boost/atomic/detail/fallback.hpp libraries/boost_aux/boost/atomic/gcc-sparcv9.hpp libraries/boost_aux/boost/atomic/detail/gcc-ppc.hpp libraries/boost_aux/boost/atomic/platform.hpp Copyright: 2009 Helge Bahmann License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/boost/atomic/detail/gcc-armv6+.hpp Copyright: 2009 Helge Bahmann 2009 Phil Endecott License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/boost/atomic/detail/linux-arm.hpp Copyright: 2009, 2011 Helge Bahmann 2009 Phil Endecott License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/boost/atomic/detail/cas32strong.hpp libraries/boost_aux/boost/atomic/detail/gcc-cas.hp libraries/boost_aux/boost/atomic/detail/cas32weak.hpp libraries/boost_aux/boost/atomic/detail/type-classifier.hpp Copyright: 2011 Helge Bahmann License: Boost Software License, Version 1.0 See above Files: libraries/boost_aux/boost/foreach_field.hpp Copyright: 2009 Chris Purcell License:Boost Software License, Version 1.0 See above Files: debian/* Copyright: 2012 Filippo Rusconi License: GPL-3+ This package 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 package 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 . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/libpwiz-dev.30000664000000000000000000000405312254744066011524 0ustar .TH "LIBPWIZ-DEV" "3" "October 2012" .SH "NAME" libpwiz-dev \- library to perform proteomics data analyses (development files) .SH "DESCRIPTION" This manual page documents briefly the \fBlibpwiz-dev\fR package that ships all the files required to develop programs that make use of the \fBlibpwiz\fR library. The \fBlibpwiz\fR library allows one to perform proteomics data analyses. The ProteoWizard project that develops \fBlibpwiz\fR provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. (2012) A cross-platform toolkit for mass spectrometry and proteomics. \fI Nature Biotechnology\fP, 30. 10.1038/nbt.2377. .SH "SEE ALSO" .BR libpwiz (3), .BR libpwiz\-doc (7), .PP The library is documented fully in the doxygen-extacted documentation that is packaged in \fBlibpwiz\-doc\fR. .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/make-included-headers-hierarchy.sh0000775000000000000000000000107012254744066015626 0ustar #!/bin/sh WORK_DIR=$PWD DEBIAN_DIR=${WORK_DIR}/debian INCLUDES_DIR=${DEBIAN_DIR}/includes/libpwiz rm -rf ${INCLUDES_DIR} for file in $(find . -type f | grep ".*\.h[p]\{0,2\}$" | sed 's|^./||') do # except files in debian/ !!! echo ${file} | grep debian if [ "$?" != "0" ] then baseName=$(basename ${file}) # echo "baseName: ${baseName}" dirName=$(dirname ${file}) # echo "dirName: ${dirName}" mkdir -p ${INCLUDES_DIR}/${dirName} cp ${file} ${INCLUDES_DIR}/${dirName} fi done debian/libpwiz-doc.lintian-overrides0000664000000000000000000000004712254744066015006 0ustar no-upstream-changelog duplicate-files debian/libpwiz-tools.install0000664000000000000000000000025312254744107013404 0ustar debian/build/usr/bin/msconvert usr/bin debian/build/usr/bin/idconvert usr/bin debian/build/usr/bin/mscat usr/bin debian/build/usr/bin/txt2mzml usr/bin debian/libpwiz-doc.doc-base0000664000000000000000000000047212254744066013027 0ustar Document: libpwiz-documentation Title: libpwiz Documentation Author: Abstract: This manual describes what libpwiz is and how it can be used to handle mass spectrometric data. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/libpwiz-doc/html/index.html Files: /usr/share/doc/libpwiz-doc/html/*.html debian/libpwiz3.dirs0000664000000000000000000000004712254744066011631 0ustar usr/lib usr/lib/libpwiz3/example-files debian/libpwiz-doc.install0000664000000000000000000000015012254744066013011 0ustar # The generated HTML-formatted documentation. doc/dox/html usr/share/doc/libpwiz-doc debian/source/0000775000000000000000000000000012254744156010502 5ustar debian/source/format0000664000000000000000000000001412254744066011710 0ustar 3.0 (quilt) debian/libpwiz-dev.links0000664000000000000000000000005512254744066012500 0ustar usr/lib/libpwiz.so.3.0.0 usr/lib/libpwiz.so debian/libpwiz-doc.manpages0000664000000000000000000000002612254744066013140 0ustar debian/libpwiz-doc.7 debian/changelog0000664000000000000000000000666312255352073011061 0ustar libpwiz (3.0.4624-6ubuntu2) trusty; urgency=medium * Switch to dh_autoreconf to get new libtool macros for ppc64el. -- Adam Conrad Sat, 21 Dec 2013 10:45:09 -0700 libpwiz (3.0.4624-6ubuntu1) trusty; urgency=medium * Merge from Debian unstable. Remaining changes: - Use dh_autotools-dev to update config.{sub,guess} for new ports. -- Logan Rosen Thu, 19 Dec 2013 23:32:13 -0500 libpwiz (3.0.4624-6) unstable; urgency=low * debian/control: add libpwiz-tools binary package to ship binaries that make use of libpwiz. Part of these binaries used to be shipped in /usr/lib/libpwiz3/example-files/, but that is a suboptimal setting (thanks to Olivier Langella for this input). * The example source code files have been moved from /usr/lib/libpwiz3/example-files/ to /usr/share/doc/libpwiz3/example-files/. -- Filippo Rusconi Wed, 04 Dec 2013 20:18:44 +0100 libpwiz (3.0.4624-5ubuntu1) trusty; urgency=medium * Merge from Debian unstable. Remaining changes: - Use dh_autotools-dev to update config.{sub,guess} for new ports. -- Logan Rosen Sat, 14 Dec 2013 02:01:56 -0500 libpwiz (3.0.4624-5) unstable; urgency=low * Set Build-Depends libboost-*-dev to (>= 1.54.0) (Closes: #731064). -- Filippo Rusconi Wed, 04 Dec 2013 15:39:59 +0100 libpwiz (3.0.4624-4) unstable; urgency=low * debian/rules: Run dh_fixperms after generating the symbols and shlibs files so that the correct permissions are set for them also. Lintian was complaining. -- Filippo Rusconi Fri, 15 Nov 2013 17:05:30 +0100 libpwiz (3.0.4624-3ubuntu1) trusty; urgency=low * Use dh_autotools-dev to update config.{sub,guess} for new ports. -- Adam Conrad Fri, 15 Nov 2013 09:59:22 +0000 libpwiz (3.0.4624-3) unstable; urgency=low * debian/control: set entries in Build-Depends about Boost libs on unversioned -dev packages (Closes: #722189). This time rebuild the binary package. -- Filippo Rusconi Thu, 14 Nov 2013 10:24:59 +0100 libpwiz (3.0.4624-2) unstable; urgency=low * debian/control: set entries in Build-Depends about Boost libs on unversioned -dev packages (Closes: #722189). -- Filippo Rusconi Wed, 30 Oct 2013 20:53:16 +0100 libpwiz (3.0.4624-1) unstable; urgency=low * New upstream release (Closes: #693044); * debian/control: Vcs-Git and Vcs-Browser now use the canonical URIs; * debian/copyright : fixes to the format and made a general overview after new upstream release; * debian/control: Standards-Version: 3.9.4; * debian/control: add dependency on autotools-dev to lift the lintian warning complaining about outdated-autotools-helper-file autotools/config.guess 2006-07-02; * add #DEBHELPER# to libpwiz3.postinst to lift the lintian complaining that maintainer-script-lacks-debhelper-token debian/libpwiz3.postinst; -- Filippo Rusconi Thu, 29 Aug 2013 16:22:04 +0200 libpwiz (3.0.4098-2) UNRELEASED; urgency=low * Initial release (Closes: #693044). * Fix to the version of the license for the debian/* files. -- Filippo Rusconi Mon, 05 Nov 2012 21:37:18 +0100 libpwiz (3.0.4098-1) experimental; urgency=low * Initial release (Closes: #693044). -- Filippo Rusconi Mon, 05 Nov 2012 21:37:18 +0100 debian/libpwiz-doc.70000664000000000000000000000327512254744066011524 0ustar .TH "LIBPWIZ\-DOC" "7" "October 2012" .SH "NAME" libpwiz\-doc \- library to perform proteomics data analyses \- documentation .SH "DESCRIPTION" This manual page documents briefly the \fBlibpwiz\-doc\fR package that brings the documentation of the libpwiz library as packaged in \fBlibpwiz\fR. The documentation is available as a set of HTML files, automatically extracted from the source code using Doxygen. .SH "EXAMPLES OF BINARIES" The \fBlibpwizX\fR package ships examples of programs built with the library. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.\-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. (2012) A cross\-platform toolkit for mass spectrometry and proteomics. \fI Nature Biotechnology\fP, 30. 10.1038/nbt.2377. .SH "SEE ALSO" .BR libpwiz (3), .BR libpwiz\-dev (3), .PP .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/compat0000664000000000000000000000000212254744066010400 0ustar 8 debian/idconvert.sgml0000664000000000000000000001067512254744107012070 0ustar 05 december 2013 IDCONVERT 1 idconvert idconvert Convert mass spectrometry identification file formats. idconvert DESCRIPTION This manual page documents briefly the idconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry protein identification data files from one format to another. OPTIONS -v | --verbose Display detailed processing progress information. -f | --filelist filename Uses the contents of filename which lists filenames. -o | --outdir dir Set the output directory ('-' for stdout) to dir. By default, the output directory is '.' (that is, the current working directory). -c | --config filename Set the configuration file to filename. -e | --ext ext Set the extension of the output files to ext. Can be mzid or pepXML or txt. --mzIdentML Write mzIdentML format (default). --pepXML Write pepXML format. --text Write hierarchical text format. EXAMPLES Convert sequest.pepXML to sequest.mzid idconvert sequest.pepXML Convert mascot.mzid to mascot.pepXML idconvert mascot.mzid --pepXML Use a configuration file idconvert xtandem.pep.xml -c config.txt RETURN VALUE The number of failed files. AUTHOR Filippo Rusconi <lopippo@debian.org> This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). 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. On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL\-3'. debian/libpwiz3.lintian-overrides0000664000000000000000000000006012254744066014321 0ustar spelling-error-in-binary no-upstream-changelog debian/rules0000775000000000000000000001164612255352044010262 0ustar #!/usr/bin/make -f # Based on the initial work of Joey Hess and Craig Small. # There are patches in the source package # include /usr/share/quilt/quilt.make # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 export DH_OPTIONS=-v CMAKE=/usr/bin/cmake DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) DEBIAN_DIR = $(CURDIR)/debian BUILD_DIR = $(DEBIAN_DIR)/build INSTALL_DIR = $(BUILD_DIR) # Path to the tools subdirectory in the top source dir to build the # documentation. export PATH := $(BUILD_DIR)/bin:$(CURDIR)/tools:$(PATH) export LD_LIBRARY_PATH := $(BUILD_DIR)/lib/:$(LD_LIBRARY_PATH) PROTEOWIZ_LIB_PACKAGE = libpwiz3 PROTEOWIZ_LIB_VERSION = 3.0.0 ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CXXFLAGS += -O0 else CXXFLAGS += -O2 endif ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) MAKEFLAGS += -j$(NUMJOBS) endif $(info "---------------------------------------") $(info NUMJOBS: $(NUMJOBS)) $(info MAKEFLAGS: $(MAKEFLAGS)) $(info DEB_BUILD_OPTIONS: $(DEB_BUILD_OPTIONS)) $(info "---------------------------------------") # Hardening stuff, see http://wiki.debian.org/Hardening # export DEB_BUILD_MAINT_OPTIONS = hardening=+all DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk CFLAGS+=$(CPPFLAGS) CXXFLAGS+=$(CPPFLAGS) # .NOTPARALLEL: .PHONY: clean clean: # unpatch dh_testdir dh_testroot dh_autoreconf_clean dh_clean rm -f debian/msconvert.1 rm -f debian/idconvert.1 rm -f debian/mscat.1 rm -f debian/txt2mzml.1 rm -rf $(BUILD_DIR) # Remove the generated includes directory: rm -rf debian/includes # Remove the generated doc/dox/html directory: rm -rf doc/dox/html build-arch-stamp: $(QUILT_STAMPFN) dh_testdir dh_prep -a dh_autoreconf mkdir -p $(BUILD_DIR) # Duplicate the source tree, since it is not easy to build the # software in a separate build directory. cp -rpf autotools libraries pwiz pwiz_tools $(BUILD_DIR) cd $(BUILD_DIR) && autotools/configure --prefix=/usr && \ VERBOSE=1 $(MAKE) && \ VERBOSE=1 DESTDIR=$(INSTALL_DIR) $(MAKE) install # Now that the build is fine and the built files installed, # remove all the RPATH stuff from these binaries. @echo "Removing the RPATH datum from the binaries." sh debian/remove-rpath-from-binaries.sh # Prepare a mirroring hierarchy for all the header files of the # project. The mirror is in debian/includes/libpwiz. @echo $(shell pwd) sh debian/make-included-headers-hierarchy.sh # Produce the man pages for both libpwiz-tools binaries docbook-to-man debian/msconvert.sgml > debian/msconvert.1 docbook-to-man debian/idconvert.sgml > debian/idconvert.1 docbook-to-man debian/mscat.sgml > debian/mscat.1 docbook-to-man debian/txt2mzml.sgml > debian/txt2mzml.1 touch build-arch-stamp # Build the documentation with doxygen in doc/dox. That creates an # html file. Note that we need the binary-arch build because the files # that go in the documentation are produced by the arch targets. build-indep-stamp: build-arch-stamp cd doc/dox && doxygen touch build-indep-stamp .PHONY: build build: build-arch-stamp build-indep-stamp .PHONY: build-indep build-indep: build-indep-stamp .PHONY: build-arch build-arch: build-arch-stamp # Build architecture-independent files here. .PHONY: binary-indep binary-indep: build-indep dh_testdir -i dh_testroot -i dh_installchangelogs -i dh_installdocs -i dh_install -i dh_installman -i dh_compress -i dh_fixperms -i dh_installdeb -i dh_lintian -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i # Build architecture-dependent files here. .PHONY: binary-arch binary-arch: build-arch dh_testdir -a dh_testroot -a dh_link dh_installchangelogs -a dh_installdocs -a dh_install -a dh_installmenu -a dh_installman -a dh_strip -a # Do not compress the example source and binary files. dh_compress -av -Xexample-files dh_installdeb -a # Generate the symbols for libs so that the call to dh_shlibdeps -a # can work finding the dependencies upon # $(PROTEOWIZ_LIB_PACKAGE). Specify the version # $(PROTEOWIZ_LIB_VERSION) of the lib because otherwise, # dpkg-gensymbols provides the full version with debian package # version $(PROTEOWIZ_LIB_VERSION)-1, which we do not want. dpkg-gensymbols -P$(DEBIAN_DIR) -p$(PROTEOWIZ_LIB_PACKAGE) \ -v$(PROTEOWIZ_LIB_VERSION) -c2 -d \ -e$(BUILD_DIR)/usr/lib/libpwiz.so.3.0.0 \ -O$(DEBIAN_DIR)/$(PROTEOWIZ_LIB_PACKAGE)/DEBIAN/symbols # Send the proper shared libs details for the library: echo "libpwiz 3 libpwiz3 (>= 3.0.4043-1)" > \ $(DEBIAN_DIR)/$(PROTEOWIZ_LIB_PACKAGE)/DEBIAN/shlibs # Run the fixperms after generating the symbols and shlibs files so # that the correct permissions are set for them also. Lintian was # complaining. dh_fixperms -a dh_lintian -a dh_shlibdeps -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a .PHONY: binary binary: binary-arch binary-indep debian/mscat.sgml0000664000000000000000000000341512254744107011174 0ustar 05 december 2013 MSCAT 1 mscat mscat Write spectrum data as simple text to the console. mscat DESCRIPTION This manual page documents briefly the mscat software shipped within the libpwiz-tools package. This program allows one to write spectrum data as simple text to the console. AUTHOR Filippo Rusconi <lopippo@debian.org> This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). 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. On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL\-3'. debian/remove-rpath-from-binaries.sh0000775000000000000000000000026512254744066014710 0ustar #!/bin/sh WORK_DIR=$PWD DEBIAN_DIR=${WORK_DIR}/debian BIN_DIR=${DEBIAN_DIR}/build/usr/bin cd ${BIN_DIR} for file in $(find -type f -executable) do chrpath -d ${file} done debian/control0000664000000000000000000001172012255352155010601 0ustar Source: libpwiz Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: The Debichem Group Uploaders: Filippo Rusconi Build-Depends: debhelper (>= 8.0.0), dh-autoreconf, dpkg-dev (>= 1.16.1~), chrpath (>= 0.13), doxygen (>= 1.8.1.2), docbook-to-man, libboost-program-options-dev (>= 1.54.0), libboost-date-time-dev (>= 1.54.0), libboost-iostreams-dev (>= 1.54.0), libboost-regex-dev (>= 1.54.0), libboost-filesystem-dev (>= 1.54.0), libboost-thread-dev (>= 1.54.0), libboost-system-dev (>= 1.54.0), libfftw3-dev (>= 3.3.2), libgd2-xpm-dev (>= 2.0.35), autotools-dev (>= 20130515.1) Standards-Version: 3.9.4 Section: libs Homepage: http://proteowizard.sourceforge.net/downloads.shtml Vcs-Git: git://anonscm.debian.org/debichem/packages/libpwiz.git Vcs-Browser: http://anonscm.debian.org/git/debichem/packages/libpwiz.git Package: libpwiz-dev Section: libdevel Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libpwiz3 (= ${binary:Version}) Suggests: libpwiz-doc Description: library to perform proteomics data analyses (devel files) The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. . The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files. . This package ships the library development files. Package: libpwiz3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: libpwiz-doc Description: library to perform proteomics data analyses (runtime) The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. . The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files. Package: libpwiz-tools Section: science Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libpwiz3 (= ${binary:Version}) Suggests: libpwiz-doc Description: ProteoWizard command line tools The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. . The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files. . This package ships command line tools that include _idconvert_ (conversion of MS identifications) and _msconvert_ (conversion of MS raw data files from/to any supported format). Package: libpwiz-doc Section: doc Architecture: all Depends: ${misc:Depends} Description: set of programs to perform proteomics data analyses (doc) The libpwiz library from the ProteoWizard project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. . The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files. . This package ships the documentation to the proteowizard software along with example programs (source code and binaries). debian/autoreconf0000664000000000000000000000001212255351602011252 0ustar autotools debian/txt2mzml.sgml0000664000000000000000000000404212254744107011663 0ustar 05 december 2013 TXT2MZML 1 txt2mzml txt2mzml Read text spectrum data and write mzML. txt2mzml DESCRIPTION This manual page documents briefly the txt2mzml software shipped within the libpwiz-tools package. This program allows one to read spectrum data as text from one input filename and output these data as mzML to another output filename. AUTHOR Filippo Rusconi <lopippo@debian.org> This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 05 december 2013). 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. On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL\-3'. debian/libpwiz3.postinst0000664000000000000000000000012312254744066012546 0ustar #!/bin/sh set -e if [ "$1" = "configure" ]; then ldconfig fi #DEBHELPER# debian/README.Debian0000664000000000000000000000063512254744066011247 0ustar libpwiz for Debian ----------------------- The directory for the included headers, located at /usr/include/libpwiz, was mirrored from the source tree during package build by the debian/make-included-headers-hierarchy.sh script. It is thus necessary to include that directory in the compilation command line with -I /usr/include/libpwiz. -- Filippo Rusconi , Mon, 12 Nov 2012 22:42:52 +0100 debian/libpwiz-dev.install0000664000000000000000000000012512254744066013024 0ustar debian/includes/libpwiz usr/include/ debian/build/usr/lib/libpwiz.a usr/lib debian/libpwiz3.manpages0000664000000000000000000000002112254744066012453 0ustar debian/libpwiz.3