Source: openms Section: science Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi 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.