debian/0000755000000000000000000000000012256106661007173 5ustar debian/openms-common.install0000644000000000000000000000006112256106661013347 0ustar share/* usr/share/openms-common/ debian/openms-common.dirs0000644000000000000000000000003012256106661012636 0ustar usr/share usr/share/doc debian/openms-common.70000644000000000000000000000357212256106661012061 0ustar .TH "OPENMS-COMMON" "7" "November 2012" .SH "NAME" openms\-common \- library for LC/MS data management and analysis - common files .SH "DESCRIPTION" This manual page documents briefly the \fBopenms\-common\fR package that ships shared data for the OpenMS software framework. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. \fI BMC Bioinformatics\fP, 9:163. doi:10.1186/1471-2105-9-163. .SH "SEE ALSO" .BR libopenms (3), .BR topp (1), .BR openms (7), .BR openms\-doc (7). .PP The program is documented fully in the \fITutorials\fP, that are packaged in \fBopenms\-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/libopenms1.11.lintian-overrides0000644000000000000000000000016212256106661015043 0ustar spelling-error-in-binary shlib-calls-exit package-name-doesnt-match-sonames shlib-missing-in-symbols-control-file debian/topp.lintian-overrides0000644000000000000000000000013312256106661013532 0ustar old-fsf-address-in-copyright-file hardening-no-fortify-functions spelling-error-in-binary debian/openms-doc.dirs0000644000000000000000000000021012256106661012113 0ustar usr/share/doc/openms-doc/ usr/share/doc/openms-doc/tutorials usr/share/doc/openms-doc/tutorials/binaries usr/share/doc/openms-doc/html debian/topp.dirs0000644000000000000000000000005112256106661011034 0ustar usr/bin usr/share/pixmaps usr/share/doc debian/topp.links0000644000000000000000000002201012256106661011212 0ustar usr/share/man/man1/topp.1 usr/share/man/man1/AccurateMassSearch.1 usr/share/man/man1/topp.1 usr/share/man/man1/AdditiveSeries.1 usr/share/man/man1/topp.1 usr/share/man/man1/BaselineFilter.1 usr/share/man/man1/topp.1 usr/share/man/man1/CVInspector.1 usr/share/man/man1/topp.1 usr/share/man/man1/CompNovo.1 usr/share/man/man1/topp.1 usr/share/man/man1/CompNovoCID.1 usr/share/man/man1/topp.1 usr/share/man/man1/ConsensusID.1 usr/share/man/man1/topp.1 usr/share/man/man1/ConsensusMapNormalizer.1 usr/share/man/man1/topp.1 usr/share/man/man1/ConvertTSVToTraML.1 usr/share/man/man1/topp.1 usr/share/man/man1/ConvertTraMLToTSV.1 usr/share/man/man1/topp.1 usr/share/man/man1/DBExporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/DBImporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/DTAExtractor.1 usr/share/man/man1/topp.1 usr/share/man/man1/DeMeanderize.1 usr/share/man/man1/topp.1 usr/share/man/man1/Decharger.1 usr/share/man/man1/topp.1 usr/share/man/man1/DecoyDatabase.1 usr/share/man/man1/topp.1 usr/share/man/man1/Digestor.1 usr/share/man/man1/topp.1 usr/share/man/man1/DigestorMotif.1 usr/share/man/man1/topp.1 usr/share/man/man1/EICExtractor.1 usr/share/man/man1/topp.1 usr/share/man/man1/ERPairFinder.1 usr/share/man/man1/topp.1 usr/share/man/man1/ExecutePipeline.1 usr/share/man/man1/topp.1 usr/share/man/man1/FFEval.1 usr/share/man/man1/topp.1 usr/share/man/man1/FalseDiscoveryRate.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderCentroided.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderIsotopeWavelet.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderMRM.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderMetabo.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderRaw.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureFinderSuperHirn.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureLinkerLabeled.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureLinkerUnlabeled.1 usr/share/man/man1/topp.1 usr/share/man/man1/FeatureLinkerUnlabeledQT.1 usr/share/man/man1/topp.1 usr/share/man/man1/FileConverter.1 usr/share/man/man1/topp.1 usr/share/man/man1/FileFilter.1 usr/share/man/man1/topp.1 usr/share/man/man1/FileInfo.1 usr/share/man/man1/topp.1 usr/share/man/man1/FileMerger.1 usr/share/man/man1/topp.1 usr/share/man/man1/FuzzyDiff.1 usr/share/man/man1/topp.1 usr/share/man/man1/GenericWrapper.1 usr/share/man/man1/topp.1 usr/share/man/man1/HighResPrecursorMassCorrector.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDConflictResolver.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDDecoyProbability.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDEvaluator.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDEvaluatorGUI.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDExtractor.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDFileConverter.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDFilter.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDMapper.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDMassAccuracy.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDMerger.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDPosteriorErrorProbability.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDRTCalibration.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDRipper.1 usr/share/man/man1/topp.1 usr/share/man/man1/IDSplitter.1 usr/share/man/man1/topp.1 usr/share/man/man1/INIFileEditor.1 usr/share/man/man1/topp.1 usr/share/man/man1/INIUpdater.1 usr/share/man/man1/topp.1 usr/share/man/man1/ITRAQAnalyzer.1 usr/share/man/man1/topp.1 usr/share/man/man1/ImageCreator.1 usr/share/man/man1/topp.1 usr/share/man/man1/InclusionExclusionListCreator.1 usr/share/man/man1/topp.1 usr/share/man/man1/InspectAdapter.1 usr/share/man/man1/topp.1 usr/share/man/man1/InternalCalibration.1 usr/share/man/man1/topp.1 usr/share/man/man1/IsobaricAnalyzer.1 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usr/share/man/man1/MyriMatchAdapter.1 usr/share/man/man1/topp.1 usr/share/man/man1/MzTabExporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/NoiseFilterGaussian.1 usr/share/man/man1/topp.1 usr/share/man/man1/NoiseFilterSGolay.1 usr/share/man/man1/topp.1 usr/share/man/man1/OMSSAAdapter.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenMSInfo.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathAnalyzer.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathChromatogramExtractor.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathConfidenceScoring.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathDIAPreScoring.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathDecoyGenerator.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathFeatureXMLToTSV.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathMzMLFileCacher.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathRTNormalizer.1 usr/share/man/man1/topp.1 usr/share/man/man1/OpenSwathRewriteToFeatureXML.1 usr/share/man/man1/topp.1 usr/share/man/man1/PILISIdentification.1 usr/share/man/man1/topp.1 usr/share/man/man1/PILISModelCV.1 usr/share/man/man1/topp.1 usr/share/man/man1/PILISModelTrainer.1 usr/share/man/man1/topp.1 usr/share/man/man1/PILISSpectraGenerator.1 usr/share/man/man1/topp.1 usr/share/man/man1/PTModel.1 usr/share/man/man1/topp.1 usr/share/man/man1/PTPredict.1 usr/share/man/man1/topp.1 usr/share/man/man1/PeakPickerHiRes.1 usr/share/man/man1/topp.1 usr/share/man/man1/PeakPickerWavelet.1 usr/share/man/man1/topp.1 usr/share/man/man1/PepNovoAdapter.1 usr/share/man/man1/topp.1 usr/share/man/man1/PeptideIndexer.1 usr/share/man/man1/topp.1 usr/share/man/man1/PhosphoScoring.1 usr/share/man/man1/topp.1 usr/share/man/man1/PrecursorIonSelector.1 usr/share/man/man1/topp.1 usr/share/man/man1/PrecursorMassCorrector.1 usr/share/man/man1/topp.1 usr/share/man/man1/ProteinInference.1 usr/share/man/man1/topp.1 usr/share/man/man1/ProteinQuantifier.1 usr/share/man/man1/topp.1 usr/share/man/man1/ProteinResolver.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCCalculator.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCEmbedder.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCExporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCExtractor.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCImporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCMerger.1 usr/share/man/man1/topp.1 usr/share/man/man1/QCShrinker.1 usr/share/man/man1/topp.1 usr/share/man/man1/RNPxl.1 usr/share/man/man1/topp.1 usr/share/man/man1/RNPxlXICFilter.1 usr/share/man/man1/topp.1 usr/share/man/man1/RTEvaluation.1 usr/share/man/man1/topp.1 usr/share/man/man1/RTModel.1 usr/share/man/man1/topp.1 usr/share/man/man1/RTPredict.1 usr/share/man/man1/topp.1 usr/share/man/man1/Resampler.1 usr/share/man/man1/topp.1 usr/share/man/man1/SILACAnalyzer.1 usr/share/man/man1/topp.1 usr/share/man/man1/SeedListGenerator.1 usr/share/man/man1/topp.1 usr/share/man/man1/SemanticValidator.1 usr/share/man/man1/topp.1 usr/share/man/man1/SequenceCoverageCalculator.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpecLibCreator.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpecLibSearcher.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterBernNorm.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterMarkerMower.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterNLargest.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterNormalizer.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterParentPeakMower.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterScaler.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterSqrtMower.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterThresholdMower.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraFilterWindowMower.1 usr/share/man/man1/topp.1 usr/share/man/man1/SpectraMerger.1 usr/share/man/man1/topp.1 usr/share/man/man1/SvmTheoreticalSpectrumGeneratorTrainer.1 usr/share/man/man1/topp.1 usr/share/man/man1/TMTAnalyzer.1 usr/share/man/man1/topp.1 usr/share/man/man1/TOFCalibration.1 usr/share/man/man1/topp.1 usr/share/man/man1/TOPPAS.1 usr/share/man/man1/topp.1 usr/share/man/man1/TOPPView.1 usr/share/man/man1/topp.1 usr/share/man/man1/TextExporter.1 usr/share/man/man1/topp.1 usr/share/man/man1/TransformationEvaluation.1 usr/share/man/man1/topp.1 usr/share/man/man1/XMLValidator.1 usr/share/man/man1/topp.1 usr/share/man/man1/XTandemAdapter.1 debian/source/0000755000000000000000000000000012256106661010473 5ustar debian/source/lintian-overrides0000644000000000000000000000005112256106661014050 0ustar maintainer-script-lacks-debhelper-token debian/source/format0000644000000000000000000000001512256106661011702 0ustar 3.0 (quilt) debian/openms-common.lintian-overrides0000644000000000000000000000004212256106661015336 0ustar package-contains-empty-directory debian/libopenms-dev.docs0000644000000000000000000000001012256106661012600 0ustar AUTHORS debian/purify-openms-svn-source-tree.sh0000644000000000000000000000066712256106661015414 0ustar #!/bin/sh -e workDir=$1 cd ${workDir} # Remove all the .svn hidden dirs (source tree was cloned off a svn # repos). find -name ".svn" | xargs rm -rvf # Remove all the exec bits from files that $(file) considers not # binary. for item in $(find -type f -executable) do file ${item} | grep -i "elf " if [ "$?" != "0" ] then echo "file ${item} not binary. Running chmod a-x on it." chmod a-x ${item} fi done debian/topp.menu0000644000000000000000000000073712256106661011052 0ustar ?package(topp):\ needs="X11"\ section="Applications/Science/Chemistry"\ title="TOPPAS"\ longtitle="Assistant for GUI-driven TOPP workflow design (OpenMS framework)"\ icon="/usr/share/pixmaps/TOPPAS.xpm"\ command="/usr/bin/TOPPAS" ?package(topp):\ needs="X11"\ section="Applications/Science/Chemistry"\ title="TOPPView"\ longtitle="Viewer for mass spectrometry data (OpenMS framework)"\ icon="/usr/share/pixmaps/TOPPView.xpm"\ command="/usr/bin/TOPPView" debian/control0000644000000000000000000002010712256106661010576 0ustar Source: openms Section: science Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi Build-Depends: debhelper (>=7.0.50~), dpkg-dev (>= 1.16.1~), cmake (>=2.6.3), libxerces-c-dev (>= 3.1.1), libgsl0-dev (>= 1.15+dfsg), libboost-dev (>= 1.54.0), libboost-iostreams-dev (>= 1.54.0), libboost-date-time-dev (>= 1.54.0), libboost-math-dev (>= 1.54.0), seqan-dev (>= 1.4.1), libsvm-dev (>= 3.12), libglpk-dev (>= 4.52.1), zlib1g-dev (>= 1.2.7), libbz2-dev (>= 1.0.6), cppcheck (>= 1.54), libqt4-dev (>= 4.8.2), libqt4-opengl-dev (>= 4.8.2), libqtwebkit-dev (>= 2.2.1), coinor-libcoinutils-dev (>= 2.6.4), imagemagick, doxygen (>= 1.8.1.2), graphviz, texlive-extra-utils, texlive-latex-extra, latex-xcolor, texlive-font-utils, ghostscript, texlive-fonts-recommended Standards-Version: 3.9.4 Homepage: http://open-ms.sourceforge.net/ Vcs-Git: git://anonscm.debian.org/debichem/packages/openms.git Vcs-Browser: http://anonscm.debian.org/git/debichem/packages/openms.git Package: libopenms1.11 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, openms-common (= ${source:Version}) Conflicts: libopenms1 Suggests: openms-doc Section: libs Description: library for LC/MS data management and analysis - runtime OpenMS is a library for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. . OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… . It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… . OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. Package: libopenms-dev Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms1.11 (= ${binary:Version}) Suggests: openms-doc Section: libdevel Description: library for LC/MS data management and analysis - dev files OpenMS is a library for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. . OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… . It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… . OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. . This package ships the library development files. Package: topp Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms1.11 (= ${binary:Version}), openms-common (= ${source:Version}) Suggests: openms-doc Description: set of programs implementing The OpenMS Proteomic Pipeline TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem. The applications make use of the libopenms library. Some examples of these applications are : . - TOPPView: A viewer for mass spectrometry data. - TOPPAS: An assistant for GUI-driven TOPP workflow design. - DTAExtractor: Extracts spectra of an MS run file to several files in DTA format. - FileConverter: Converts between different MS file formats. - FileFilter: Extracts or manipulates portions of data from peak, feature or consensus feature files. - SpectraMerger: Merges spectra from an LC/MS map, either by precursor or by RT blocks. - BaselineFilter: Removes the baseline from profile spectra using a top-hat filter. - InternalCalibration: Applies an internal calibration. - PTModel: Trains a model for the prediction of proteotypic peptides from a training set. - RTPredict: Predicts retention times for peptides using a model trained by RTModel. - ExecutePipeline: Executes workflows created by TOPPAS. Package: openms-common Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: libopenms1.11 (= ${binary:Version}), topp (= ${binary:Version}) Description: package for LC/MS data management and analysis - shared data OpenMS is a package for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. . OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… . It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… . OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. . This package brings data shared by the different binaries of the OpenMS software package (libOpenMS and libOpenMS_GUI libraries and the OpenMS Proteomic Pipeline binary tools). Package: openms-doc Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, libjs-jquery Suggests: libopenms1.11 (= ${binary:Version}), topp (= ${binary:Version}) Section: doc Description: package for LC/MS data management and analysis - documentation OpenMS is a package for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. . OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… . It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… . OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. . This package brings full documentation for both the libopenms library package (libOpenMS and libOpenMS_GUI) and the OpenMS Proteomic Pipeline (topp) package. Package: openms Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms1.11 (>= ${source:Version}), topp (>= ${source:Version}), Suggests: openms-doc1.11 Description: package for LC/MS data management and analysis OpenMS is a package for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. . TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem. . This package is a metapackage that depends on both the libopenms library package (libOpenMS and libOpenMS_GUI) and the OpenMS Proteomic Pipeline (topp) package. debian/openms-doc.install0000644000000000000000000000056712256106661012637 0ustar debian/build/doc/OpenMS_tutorial.pdf usr/share/doc/openms-doc/tutorials debian/build/doc/TOPP_tutorial.pdf usr/share/doc/openms-doc/tutorials debian/build/bin/Tutorial* usr/share/doc/openms-doc/tutorials/binaries debian/build/doc/index.html usr/share/doc/openms-doc debian/build/doc/html usr/share/doc/openms-doc debian/compat0000644000000000000000000000000212256106661010371 0ustar 7 debian/libopenms-dev.links0000644000000000000000000000025412256106661013002 0ustar usr/lib/libOpenMS.so.1.11.1 usr/lib/libOpenMS.so usr/lib/libOpenMS_GUI.so.1.11.1 usr/lib/libOpenMS_GUI.so usr/lib/libOpenSwathAlgo.so.1.11.1 usr/lib/libOpenSwathAlgo.so debian/openms.manpages0000644000000000000000000000002012256106661012201 0ustar debian/openms.7 debian/openms.docs0000644000000000000000000000001012256106661011335 0ustar AUTHORS debian/libopenms-dev.install0000644000000000000000000000056712256106661013337 0ustar include/OpenMS usr/include debian/build/include/OpenMS/config.h usr/include/OpenMS debian/build/include/OpenMS/openms_package_version.h usr/include/OpenMS debian/build/include/OpenMS/openms_svn_revision.h usr/include/OpenMS cmake/*.cmake usr/share/libopenms-dev/cmake debian/libopenms1.11.postinst0000644000000000000000000000010712256106661013267 0ustar #!/bin/sh set -e if [ "$1" = "configure" ]; then ldconfig fi debian/upstream0000644000000000000000000000106212256106661010755 0ustar Reference: Author: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher Title: OpenMS – an Open-Source Software Framework for Mass Spectrometry Journal: BMC Bioinformatics Year: 2008 Volume: 9 Number: 163 DOI: 10.1186/1471-2105-9-163 PMID: 18366760 URL: http://www.biomedcentral.com/1471-2105/9/163 eprint: http://www.biomedcentral.com/content/pdf/1471-2105-9-163.pdf Repository: http://open-ms.sourceforge.net/ debian/libopenms-dev.dirs0000644000000000000000000000007012256106661012617 0ustar usr/include usr/share/libopenms-dev/cmake usr/share/doc debian/patches/0000755000000000000000000000000012256106661010622 5ustar debian/patches/series0000644000000000000000000000007512256106661012041 0ustar doc-path-for-debian.patch debian-specific-build-config.patch debian/patches/doc-path-for-debian.patch0000644000000000000000000000471312256106661015353 0ustar This patch ensures that the documentation will be available in a standard location on Debian GNU/Linux systems. This patch was designed and applied by the packager, Filippo Rusconi . --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -284,6 +284,9 @@ include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/svnversion.cmake) # generate the header once (for VersionInfo.C include) endif() +# At this point make a summary of where data and doc will be located: +message(STATUS "Info: CF_OPENMS_DATA_PATH: ${CF_OPENMS_DATA_PATH}") +message(STATUS "Info: CF_OPENMS_DOC_PATH: ${CF_OPENMS_DOC_PATH}") ######################################################## ### configure config.h ### --- a/cmake/OpenMSBuildSystem_configh.cmake +++ b/cmake/OpenMSBuildSystem_configh.cmake @@ -2,14 +2,14 @@ ## define some directories if ("${INSTALL_PREFIX}" STREQUAL ".") set(CF_OPENMS_DATA_PATH ${PROJECT_SOURCE_DIR}/share/OpenMS CACHE INTERNAL "Path to the shared documents of OpenMS.") + set(CF_OPENMS_DOC_PATH ${PROJECT_SOURCE_DIR}/doc CACHE INTERNAL "Path to the documentation of OpenMS.") set(CMAKE_INSTALL_PREFIX ${PROJECT_SOURCE_DIR}) else() set(CF_OPENMS_DATA_PATH ${INSTALL_PREFIX}/share/OpenMS CACHE INTERNAL "Path to the shared documents of OpenMS.") + set(CF_OPENMS_DOC_PATH ${INSTALL_PREFIX}/doc CACHE INTERNAL "Path to the documentation of OpenMS.") set(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX}) endif() - - set(CF_OPENMS_TEST_DATA_PATH ${PROJECT_SOURCE_DIR}/source/TEST/data/ CACHE INTERNAL "Path to the test data") ## check for Microsoft Visual Studio compiler --- a/include/OpenMS/config.h.in +++ b/include/OpenMS/config.h.in @@ -53,6 +53,9 @@ // The path to the directory where OpenMS data is installed #define OPENMS_DATA_PATH "@CF_OPENMS_DATA_PATH@" +// The path to the directory where OpenMS doc is installed +#define OPENMS_DOC_PATH "@CF_OPENMS_DOC_PATH@" + // The directory where OpenMS is build #define OPENMS_SOURCE_PATH "@PROJECT_SOURCE_DIR@" --- a/source/SYSTEM/File.C +++ b/source/SYSTEM/File.C @@ -286,6 +286,9 @@ search_dirs.push_back(String(OPENMS_BINARY_PATH) + "/doc/"); search_dirs.push_back(String(OPENMS_SOURCE_PATH) + "/doc/"); search_dirs.push_back(getOpenMSDataPath() + "/../../doc/"); +#ifdef OPENMS_DOC_PATH + search_dirs.push_back(String(OPENMS_DOC_PATH)); +#endif // needed for OpenMS Mac OS X packages where documentation is stored in /Documentation #if defined(__APPLE__) debian/patches/debian-specific-build-config.patch0000644000000000000000000000342012256106661017207 0ustar This patch ensures that the package builds correctly for Debian GNU/Linux systems. diff --git a/CMakeLists.txt b/CMakeLists.txt index 6e647b3..83a7982 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -514,6 +514,30 @@ endforeach(i) add_custom_target(doc_progs) add_dependencies(doc_progs ${OpenMS_doc_executables} TOPP UTILS GUI) +if(DEBIAN_BUILD) +## Official Debian stuff by Filippo Rusconi +## This stuff was put here after the suggestion made by +## Hannes Roest (release manager of the upstream project). + +# No RPATH at all in any of the binaries built here: +set (CMAKE_SKIP_RPATH TRUE) +MESSAGE(STATUS "Official Debian packaging recognized") +MESSAGE(STATUS "CMAKE_SKIP_RPATH: ${CMAKE_SKIP_RPATH}") + +# Let's have the lib version and the soversion in +# the lib filename. No symlinking upon install. +set(OPENMS_VSTRING "${OPENMS_PACKAGE_VERSION_MAJOR}.${OPENMS_PACKAGE_VERSION_MINOR}.${OPENMS_PACKAGE_VERSION_PATCH}") +set_target_properties(OpenMS PROPERTIES VERSION ${OPENMS_VSTRING} SOVERSION ${OPENMS_VSTRING}) +install(TARGETS OpenMS LIBRARY DESTINATION lib NAMELINK_SKIP) +set_target_properties(OpenMS_GUI PROPERTIES VERSION ${OPENMS_VSTRING} SOVERSION ${OPENMS_VSTRING}) +install(TARGETS OpenMS_GUI LIBRARY DESTINATION lib NAMELINK_SKIP) +set_target_properties(OpenSwathAlgo PROPERTIES VERSION ${OPENMS_VSTRING} SOVERSION ${OPENMS_VSTRING}) +install(TARGETS OpenSwathAlgo LIBRARY DESTINATION lib NAMELINK_SKIP) + +# Force *.so to be used, not *.a. +set(CMAKE_FIND_LIBRARY_SUFFIXES ".so") +endif() + ##### CTDs #### # We will use this path for the knime packages and the osx installer set(SEARCH_ENGINES_DIRECTORY "" CACHE PATH "Directory containing the search engine executables that should be shipped with OpenMS. Note: We expect the layout from the SVN.") debian/TOPPView.desktop0000644000000000000000000000051312256106661012202 0ustar [Desktop Entry] Name=TOPPView Categories=Science;Biology;Chemistry; Comment=viewer for mass spectrometry data Exec=TOPPView %U Icon=/usr/share/pixmaps/TOPPView.xpm Terminal=false Type=Application StartupNotify=true Name[fr_FR]=TOPPView Keywords=mass spectrometry;proteomics; Keywords[fr_FR]=spectrométrie de masse;protéomique; debian/topp.1-bottom-skel0000644000000000000000000000172012256106661012475 0ustar .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. \fI BMC Bioinformatics\fP, 9:163. doi:10.1186/1471-2105-9-163. .SH "SEE ALSO" .BR libopenms (3), .BR openms-common (7), .BR openms (7), .BR openms\-doc (7). .PP The program is documented fully in the \fITutorials\fP, that are packaged in openms\-doc. .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/purify-source-tree.sh0000755000000000000000000000123412256106661013303 0ustar #!/bin/sh echo $(pwd) # Remove all unwanted files/dirs. echo "Now removing the whole contrib directory" find . -name "contrib" -type d -exec rm -rfv '{}' \; > /dev/null 2>&1 echo "Now removing the whole .svn directory" find . -name ".svn" -type d -exec rm -rfv '{}' \; > /dev/null 2>&1 echo "Now removing all the .exe files" find . -name "*.exe" -type f -exec rm -rvf '{}' \; # Remove all the exec bits from files that $(file) considers not # binary. for item in $(find -type f -executable) do file ${item} | grep -i "elf " if [ "$?" != "0" ] then echo "file ${item} not binary. Running chmod a-x on it." chmod a-x ${item} fi done debian/libopenms.30000644000000000000000000000353612256106661011256 0ustar .TH "LIBOPENMS" "3" "October 2012" .SH "NAME" libopenms \- library for LC/MS data management and analysis .SH "DESCRIPTION" This manual page documents briefly the \fBlibopenms\fR package that brings a library for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. \fI BMC Bioinformatics\fP, 9:163. doi:10.1186/1471-2105-9-163. .SH "SEE ALSO" .BR topp (1), .BR openms-common (7), .BR openms (7), .BR openms\-doc (7). .PP The program is documented fully in the \fITutorials\fP, that are packaged in openms\-doc. .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/libopenms1.11.links0000644000000000000000000000026712256106661012533 0ustar usr/lib/libOpenMS.so.1.11.1 usr/lib/libOpenMS.so.1 usr/lib/libOpenMS_GUI.so.1.11.1 usr/lib/libOpenMS_GUI.so.1 usr/lib/libOpenSwathAlgo.so.1.11.1 usr/lib/libOpenSwathAlgo.so.1 debian/openms.70000644000000000000000000000367012256106661010572 0ustar .TH "OPENMS" "7" "November 2012" .SH "NAME" openms \- library for LC/MS data management and analysis - metapackage .SH "DESCRIPTION" This manual page documents briefly the \fBopenms\fR metapackage that depends on all the components of the OpenMS software framework but the \fBopenms\-doc\fR documentation package. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. \fI BMC Bioinformatics\fP, 9:163. doi:10.1186/1471-2105-9-163. .SH "SEE ALSO" .BR libopenms (3), .BR topp (1), .BR openms-common (7), .BR openms (7), .BR openms\-doc (7). .PP The program is documented fully in the \fITutorials\fP, that are packaged in \fBopenms\-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/openms-doc.70000644000000000000000000000346212256106661011334 0ustar .TH "OPENMS-DOC" "7" "November 2012" .SH "NAME" openms\-doc \- library for LC/MS data management and analysis - documentation .SH "DESCRIPTION" This manual page documents briefly the \fBopenms\-doc\fR package that brings a full set of documentation and tutorials to the OpenMS software framework. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. .SH "BIBLIOGRAPHICAL REFERENCE TO BE CITED" Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software Framework for Mass Spectrometry. \fI BMC Bioinformatics\fP, 9:163. doi:10.1186/1471-2105-9-163. .SH "SEE ALSO" .BR libopenms (3), .BR topp (1), .BR openms-common (7), .BR openms (7), .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/openms-doc.doc-base.libopenms-tutorial0000644000000000000000000000072312256106661016470 0ustar Document: libopenms-documentation Title: libOpenMS mass spectrometry library documentation Author: Dr Oliver Kohlbacher and Colleagues Abstract: This documentation describes the uses and features of the libOpenMS mass spectrometry library (package libopenms) Section: Science/Chemistry Format: PDF Files: /usr/share/doc/openms-doc/tutorials/OpenMS_tutorial.pdf Format: HTML Index: /usr/share/doc/openms-doc/index.html Files: /usr/share/doc/openms-doc/html/*.html debian/binaries-extract-one-line-man-desc.sh0000755000000000000000000000213012256106661016163 0ustar #!/bin/sh -e binDir="build/bin" cd ${binDir} manPage="../../topp.1" debLinkFile="../../topp.links" # Start fresh rm -f ${debLinkFile} # List all files in here, but not the Tutorial* binaries. # Add a dot to the end of each line, where missing. # First cat the top part of the man page to a temp file cat ../../topp.1-top-skel > ${manPage} # Now make the one-liners appear after the top. Note that each time a # new binary is dealt with, we create a corresponding link in # ${debLinkFile}, as each binary must have a corresponding man page. for file in $(find * -type f -executable -print | grep -v ^Tutorial) do # The man page itself oneLiner=$(./$file --help 2>&1 | grep "${file} --" | sed "s|\([^\.]$\)|\1.|g") formattedOneLiner=$(echo "${oneLiner}" | sed 's|\(^[[:alnum:]]\+\)|\\\\fB\1\\\\fR|g') echo ${formattedOneLiner} >> ${manPage} echo "" >> ${manPage} # The symbolic link echo "usr/share/man/man1/topp.1 usr/share/man/man1/${file}.1" >> ${debLinkFile} done # Finally make the bottom of the page. cat ../../topp.1-bottom-skel >> ${manPage} cd - > /dev/null 2>&1 debian/openms-doc.manpages0000644000000000000000000000002412256106661012750 0ustar debian/openms-doc.7 debian/topp.docs0000644000000000000000000000001012256106661011016 0ustar AUTHORS debian/openms-common.docs0000644000000000000000000000001012256106661012623 0ustar AUTHORS debian/copyright0000644000000000000000000000536012256106661011132 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: openms Upstream-Contact: Oliver Kohlbacher Source: http://open-ms.sourceforge.net/ Files: * Copyright: 2003-2013 The OpenMS Team -- Eberhard Karls University Tuebingen Copyright: 2003-2013 The OpenMS Team -- ETH Zurich Copyright: 2003-2013 The OpenMS Team -- Freie Universitaet Berlin License: BSD This software is released under a three-clause BSD license: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 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. * Neither the name of any author or any participating institution may be used to endorse or promote products derived from this software without specific prior written permission. . For a full list of authors, refer to the file AUTHORS. -------------------------------------------------------------------------- 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 ANY OF THE AUTHORS OR THE CONTRIBUTING INSTITUTIONS 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: debian/* Copyright: 2012 Filippo Rusconi (lopippo@debian.org) 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 program. If not, see . . 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/topp.1-top-skel0000644000000000000000000000167412256106661012003 0ustar .TH "TOPP" "1" "November 2012" .SH "NAME" topp \- library for LC/MS data management and analysis - tools .SH "DESCRIPTION" This manual page documents briefly the \fBtopp\fR package that brings a set of binary tools to build the OpenMS proteomics pipeline (topp). OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH… It provides build-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling. .SH "AVAILABLE MODULES" debian/rules0000755000000000000000000001540712256106661010262 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 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) DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) DEBIAN_DIR = $(CURDIR)/debian BUILD_DIR = $(DEBIAN_DIR)/build # 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) OPENMS_LIB_PACKAGE = libopenms1.11 OPENMS_LIB_VERSION = 1.11.1 ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CXXFLAGS += -O0 else CXXFLAGS += -O2 endif # Commented out to check if the parallel build mode triggers "race # conditions" with the linker trying to link an incomplete set of # object files. # Although the .NOTPARALLEL: special make target below should do # enough by itself. # 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: dh_testdir dh_testroot dh_clean rm -rf $(BUILD_DIR) # Remove the generated xpm icon files: rm -f debian/TOPPAS.xpm rm -f debian/TOPPView.xpm # Remove the generated topp.1 man page: rm -f debian/topp.1 build-arch-stamp: dh_testdir dh_prep -a mkdir -p $(BUILD_DIR) # On the command line, use # -DCONTRIB_LIB_DIR="/usr/lib/$(dpkg-architecture -qDEB_BUILD_GNU_TYPE);/usr/lib/$(dpkg-architecture -qDEB_HOST_MULTIARCH);" # see debian/changelog for the rationale. @echo "DEB_BUILD_GNU_TYPE: $(DEB_BUILD_GNU_TYPE)" @echo "DEB_HOST_MULTIARCH: $(DEB_HOST_MULTIARCH)" cd $(BUILD_DIR) && \ $(CMAKE) -DCMAKE_FIND_LIBRARY_SUFFIXES=".so" \ -DCONTRIB_LIB_DIR="/usr/lib;/usr/lib/$(DEB_BUILD_GNU_TYPE);/lib/$(DEB_BUILD_GNU_TYPE);/usr/lib/$(DEB_HOST_MULTIARCH);/lib/$(DEB_HOST_MULTIARCH)" \ -DCF_OPENMS_DATA_PATH=/usr/share/openms-common/OpenMS/ \ -DCF_OPENMS_DOC_PATH=/usr/share/doc/openms-doc/ \ -DCMAKE_BUILD_TYPE=release \ -DDEBIAN_BUILD=ON -DBOOST_USE_STATIC=OFF ../.. # Build the libs and executable binaries VERBOSE=1 $(MAKE) -C $(BUILD_DIR) \ OpenMS TOPP UTILS GUI test_build Tutorials_build # Prepare the xpm-formatted pixmaps for the Debian menu system. # Setting imagemagick to Build-Depends, for use of convert. convert source/VISUAL/ICONS/TOPPAS.png -resize 32x32 debian/TOPPAS.xpm convert source/VISUAL/ICONS/TOPPView.png -resize 32x32 debian/TOPPView.xpm # Prepare the topp.1 man page with all the one-line description got # from calling individually each program in $(BUILD_DIR)/bin with # --help switch. The newly built libs need be in the path so that the # binaries can execute. Same for the shared data path, because the # binaries need it to run. Note the calling in sh ./ with the script # shell being itself executable, otherwise git-buildpackage would # fail. @echo $(shell pwd) cd $(DEBIAN_DIR) && \ OPENMS_DATA_PATH=$(CURDIR)/share/OpenMS/ \ LD_LIBRARY_PATH=$(BUILD_DIR)/lib/:$(LD_LIBRARY_PATH)\ sh ./binaries-extract-one-line-man-desc.sh # Build the documentation, which needs a running XWindow server. We # thus use the doc_minimal target. cd $(BUILD_DIR) && \ $(CMAKE) -DCMAKE_FIND_LIBRARY_SUFFIXES=".so" \ -DCONTRIB_LIB_DIR="/usr/lib;/usr/lib/$(DEB_BUILD_GNU_TYPE);/lib/$(DEB_BUILD_GNU_TYPE);/usr/lib/$(DEB_HOST_MULTIARCH);/lib/$(DEB_HOST_MULTIARCH)" \ -DCF_OPENMS_DATA_PATH=/usr/share/openms-common/OpenMS/ \ -DCF_OPENMS_DOC_PATH=/usr/share/doc/openms-doc/ \ -DCMAKE_BUILD_TYPE=release \ -DDEBIAN_BUILD=ON -DBOOST_USE_STATIC=OFF ../.. VERBOSE=1 LD_LIBRARY_PATH=$(BUILD_DIR)/lib/:$(LD_LIBRARY_PATH)\ PATH=$(BUILD_DIR)/bin:$(CURDIR)/tools:$(PATH)\ OPENMS_DATA_PATH=$(CURDIR)/share/OpenMS/ \ $(MAKE) -C $(BUILD_DIR) doc_minimal doc_tutorials # There are two files that we do not want to ship because # they exist in their own Debian packages. rm -f $(BUILD_DIR)/doc/html/jquery.js touch build-arch-stamp # Note that this requires a build of the binary arch stuff. build-indep-stamp: build-arch-stamp 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 CHANGELOG dh_installdocs -i dh_install -i dh_installman -i dh_compress -XOpenMS_tutorial.pdf -XTOPP_tutorial.pdf -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 CHANGELOG dh_installdocs -a dh_install -a # Now that install has been performed, remove all the Tutorial* # binaries that will not ship in the topp package, but in the # openms-doc package. rm -vf $(DEBIAN_DIR)/topp/usr/bin/Tutorial* dh_installmenu -a dh_installman -a dh_strip -a dh_compress -a dh_fixperms -a dh_installdeb -a # Generate the symbols for libs so that the call to dh_shlibdeps -a # can work finding the dependencies upon # $(OPENMS_LIB_PACKAGE). Specify the version (like x.yy.z) of the lib # because otherwise, dpkg-gensymbols provides the full version with # debian package version (x.yy.z-1), which we do not want. dpkg-gensymbols -P$(DEBIAN_DIR) -p$(OPENMS_LIB_PACKAGE) \ -v$(OPENMS_LIB_VERSION) -c2 -d \ -e$(BUILD_DIR)/lib/libOpenMS.so.$(OPENMS_LIB_VERSION) \ -e$(BUILD_DIR)/lib/libOpenMS.so.$(OPENMS_LIB_VERSION) \ -e$(BUILD_DIR)/lib/libOpenSwathAlgo.so.$(OPENMS_LIB_VERSION) \ -O$(DEBIAN_DIR)/$(OPENMS_LIB_PACKAGE)/DEBIAN/symbols # Send the proper shared libs details for the library: echo "libOpenMS 1.11.1 libopenms1.11 (>= 1.11.1-1)" > \ $(DEBIAN_DIR)/$(OPENMS_LIB_PACKAGE)/DEBIAN/shlibs echo "libOpenMS_GUI 1.11.1 libopenms1.11 (>= 1.11.1-1)" >> \ $(DEBIAN_DIR)/$(OPENMS_LIB_PACKAGE)/DEBIAN/shlibs echo "libOpenSwathAlgo 1.11.1 libopenms1.11 (>= 1.11.1-1)" >> \ $(DEBIAN_DIR)/$(OPENMS_LIB_PACKAGE)/DEBIAN/shlibs dh_lintian -a dh_shlibdeps -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a .PHONY: binary binary: binary-arch binary-indep debian/topp.install0000644000000000000000000000031612256106661011545 0ustar debian/build/bin/* usr/bin debian/TOPPView.xpm usr/share/pixmaps debian/TOPPAS.xpm usr/share/pixmaps debian/TOPPAS.desktop usr/share/applications debian/TOPPView.desktop usr/share/applications debian/libopenms1.11.install0000644000000000000000000000026212256106661013054 0ustar debian/build/lib/libOpenMS.so.1.11.1 usr/lib debian/build/lib/libOpenMS_GUI.so.1.11.1 usr/lib debian/build/lib/libOpenSwathAlgo.so.1.11.1 usr/lib debian/openms-doc.docs0000644000000000000000000000001012256106661012100 0ustar AUTHORS debian/libopenms1.11.dirs0000644000000000000000000000002712256106661012346 0ustar usr/lib usr/share/doc/ debian/topp.manpages0000644000000000000000000000001612256106661011667 0ustar debian/topp.1 debian/watch0000644000000000000000000000007312256106661010224 0ustar version=3 http://sf.net/open-ms/OpenMS-([\d\.]+)\.tar\..* debian/TOPPAS.desktop0000644000000000000000000000050312256106661011572 0ustar [Desktop Entry] Name=TOPPAS Categories=Science;Biology;Chemistry; Comment=viewer for mass spectrometry data Exec=TOPPAS %U Icon=/usr/share/pixmaps/TOPPAS.xpm Terminal=false Type=Application StartupNotify=true Name[fr_FR]=TOPPAS Keywords=mass spectrometry;proteomics; Keywords[fr_FR]=spectrométrie de masse;protéomique; debian/changelog0000644000000000000000000000514412256106661011051 0ustar openms (1.11.1-3) unstable; urgency=low * remove version number from libbost development package names; * ensure that AUTHORS is correctly shipped in all packages. -- Filippo Rusconi Fri, 20 Dec 2013 11:30:16 +0100 openms (1.11.1-2) unstable; urgency=low * New upstream release. * debian/control: canonicalize the Vcs-Git and Vcs-Browser fields; * debian/control: remove the Conflicts declaration for -dev, which is not required at all; * add *.desktop files to reference OpenMS in the non-Debian menus (thanks to Olivier Langella). Note that preexisting topp.menu shows the menus in the Debian menu if menu-xdg is installed. Sent enquiry about having these two files included in upstream. * Standards-Version: 3.9.4; -- Filippo Rusconi Thu, 19 Dec 2013 09:41:22 +0100 openms (1.11.0-1) UNRELEASED; urgency=low * New upstream release. -- Filippo Rusconi Wed, 10 Jul 2013 22:54:41 +0200 openms (1.10.0-1) UNRELEASED; urgency=low * New upstream release. -- Filippo Rusconi Wed, 10 Jul 2013 22:54:41 +0200 openms (1.9.0-4) unstable; urgency=low * debian/rules: reinstate the .NOTPARALLEL: directive to preclude parallelization of the build, as the errors are too complicated to follow in the build log. Also inhibit the parallel=%,$(DEB_BUILD_OPTIONS) and NUMJOBS options processing, as suggested by Aaron M. Ucko" (Closes: #702606). -- Filippo Rusconi Fri, 29 Mar 2013 13:05:15 +0100 openms (1.9.0-3) unstable; urgency=low * debian/rules: fix problem with DEB_BUILD_GNU_TYPE not holding proper values on some platforms, like i386, by adding DEB_HOST_MULTIARCH. Thanks to "Aaron M. Ucko" (Closes: #702512); * Fix the watch file, thanks to Nick Black (Closes: #702518); * New code in patch ensures that there is no creation of symlinks by CMake after building of the libraries, since the symlinks are created anyways in debian/. -- Filippo Rusconi Thu, 07 Mar 2013 18:38:56 +0100 openms (1.9.0-2) unstable; urgency=low * Transition from experimental to unstable. Tests were positive. * Fix non-inclusion of generated config include files in the /usr/include/OpenMS directory -- Filippo Rusconi Wed, 06 Mar 2013 14:11:11 +0100 openms (1.9.0-1) experimental; urgency=low * 1.9.0 First Debian package release (Closes: #691129). -- Filippo Rusconi Mon, 12 Nov 2012 15:58:12 +0100 debian/openms-doc.lintian-overrides0000644000000000000000000000002112256106661014610 0ustar duplicate-files debian/openms-common.manpages0000644000000000000000000000002712256106661013476 0ustar debian/openms-common.7 debian/libopenms1.11.manpages0000644000000000000000000000002412256106661013175 0ustar debian/libopenms.3 debian/libopenms1.11.docs0000644000000000000000000000001012256106661012325 0ustar AUTHORS debian/openms-doc.doc-base.topp-tutorial0000644000000000000000000000047512256106661015466 0ustar Document: topp-documentation Title: TOPP documentation Author: Dr Oliver Kohlbacher and Colleagues Abstract: This documentation describes the uses and features of the TOPP mass spectrometry software (package topp) Section: Science/Chemistry Format: PDF Files: /usr/share/doc/openms-doc/tutorials/TOPP_tutorial.pdf