Source: openms
Section: science
Priority: optional
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Build-Depends: debhelper-compat (= 12),
dh-exec (>= 0.3),
dpkg-dev (>= 1.19.7),
cmake (>= 3.1.2),
libxerces-c-dev (>= 3.2.2),
libeigen3-dev,
libwildmagic-dev (>=5.17),
libboost-dev,
libboost-iostreams-dev,
libboost-date-time-dev,
libboost-math-dev,
libsqlite3-dev,
libsvm-dev (>= 3.21),
libglpk-dev (>= 4.65),
zlib1g-dev (>= 1.2.7),
libbz2-dev (>= 1.0.6),
cppcheck (>= 1.54),
qtbase5-dev (>= 5.11.3),
libqt5opengl5-dev (>= 5.11.3),
libqt5svg5-dev (>= 5.11.3),
coinor-libcbc-dev (>= 2.9.9),
coinor-libcgl-dev (>= 0.59.10),
libhdf5-dev,
imagemagick,
doxygen (>= 1.8.13),
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: 4.5.0
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: libopenms2.6.0
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
openms-common (= ${source:Version})
Breaks: libopenms2.5.0
Replaces: libopenms2.5.0
Conflicts: libopenms2.5.0
Suggests: openms-doc
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
Multi-Arch: same
Depends: ${misc:Depends},
libopenms2.6.0 (= ${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},
libopenms2.6.0 (= ${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
Multi-Arch: foreign
Depends: ${misc:Depends}
Suggests: libopenms2.6.0 (= ${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
Replaces: openms-doc (<= ${source:Version})
Suggests: libopenms2.6.0 (= ${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},
libopenms2.6.0 (>= ${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.