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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 (>= 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.
|
