Source: openms
Section: science
Priority: optional
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
XSBC-Original-Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper (>= 9.20151004),
               dpkg-dev (>= 1.16.1~),
               cmake (>= 3.0.2),
               libxerces-c-dev (>= 3.1.1),
               libeigen3-dev,
               libwildmagic-dev,
               libboost-dev (>= 1.54.0),
               libboost-iostreams-dev (>= 1.54.0),
               libboost-date-time-dev (>= 1.54.0),
               libboost-math-dev (>= 1.54.0),
               libsqlite3-dev,
               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),
               qtbase5-dev (>= 5.7.0),
							 libqt5opengl5-desktop-dev (>= 5.7.0),
               libqt5svg5-dev (>= 5.7.0),
               coinor-libcbc-dev (>= 2.8.12-1+b2),
               coinor-libcgl-dev (>= 0.58.9-1+b1),
               imagemagick,
               doxygen (>= 1.8.1.2),
               graphviz,
               texlive-extra-utils,
               texlive-latex-extra,
               texlive-latex-recommended,
               texlive-fonts-extra,
               texlive-font-utils,
               texlive-plain-generic,
               tex-gyre,
               ghostscript,
               texlive-fonts-recommended
Standards-Version: 4.2.1
Homepage: http://www.openms.de
Vcs-Browser: https://salsa.debian.org/debichem-team/openms
Vcs-Git: https://salsa.debian.org/debichem-team/openms.git


Package: libopenms2.4.0
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         openms-common (= ${source:Version})
Breaks: libopenms-1.11, libopenms2.0, libopenms2.3
Replaces: libopenms-1.11, libopenms2.0, libopenms2.3
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: ${misc:Depends},
         libopenms2.4.0 (= ${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},
         libopenms2.4.0 (= ${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: ${misc:Depends}
Suggests: libopenms2.4.0 (= ${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: ${misc:Depends},
         libjs-jquery
Suggests: libopenms2.4.0 (= ${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: ${misc:Depends},
         libopenms2.4.0 (>= ${source:Version}),
         topp (>= ${source:Version})
Suggests: openms-doc
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.
