Commit 59069c84 authored by Filippo Rusconi's avatar Filippo Rusconi

New upstream version 2.0.0

parent 41edef03

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

qrc_resources.cxx
DartConfiguration.tcl
/*.cmake
Testing
CMakeCache.txt
contrib
CMakeFiles
Makefile
lib
bin
build
*.user
*.pyc
moc_*.cxx*
.idea
language: cpp
compiler:
- gcc
- clang
cache: apt
before_script:
./tools/lnx-cibuild.before.sh
script:
./tools/lnx-cibuild.sh
env:
- ENABLE_STYLE_TESTING=On ENABLE_UNITYBUILD=Off WITH_GUI=On
#- ENABLE_STYLE_TESTING=Off ENABLE_UNITYBUILD=On WITH_GUI=On
- ENABLE_STYLE_TESTING=Off ENABLE_UNITYBUILD=Off WITH_GUI=On
- ENABLE_STYLE_TESTING=Off ENABLE_UNITYBUILD=Off WITH_GUI=Off
matrix:
exclude:
- env: ENABLE_STYLE_TESTING=On ENABLE_UNITYBUILD=Off WITH_GUI=On
compiler: clang
# - env: ENABLE_STYLE_TESTING=Off ENABLE_UNITYBUILD=On WITH_GUI=On
# compiler: gcc
- env: ENABLE_STYLE_TESTING=Off ENABLE_UNITYBUILD=Off WITH_GUI=Off
compiler: gcc
......@@ -5,6 +5,7 @@
The following authors contributed to OpenMS at some point. For the
authors contributing to a specific piece of code, please refer to
the authors tag in the respective file header.
- Alexandra Scherbart
- Alexandra Zerck
- Andreas Bertsch
- Anton Pervukhin
......@@ -19,6 +20,7 @@ the authors tag in the respective file header.
- Erhan Kenar
- Eva Lange
- Fabian Kriegel
- Florian Zeller
- Frederic Lehnert
- George Rosenberger
- Guillaume Belz
......@@ -29,18 +31,21 @@ the authors tag in the respective file header.
- Holger Plattfaut
- Immanuel Luhn
- Johannes Junker
- Johan Teleman
- Katharina Albers
- Knut Reinert
- Lars Nilse
- Lucia Espona
- Marc Sturm
- Lukas Mueller
- Marcel Schilling
- Marc Sturm
- Markus Mueller
- Martin Langwisch
- Mathias Walzer
- Nico Pfeifer
- Oiver Kohlbacher
- Ole Schulz-Trieglaff
- Oliver Kohlbacher
- Peter Kunszt
- Rene Hussong
- Sandro Andreotti
- Steffen Sass
......@@ -49,7 +54,4 @@ the authors tag in the respective file header.
- Timo Sachsenberg
- Vipul Patel
- Volker Mosthaf
- Lukas Mueller
- Markus Mueller
- Florian Zeller
- Peter Kunszt
- Witold Wolski
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......@@ -2,7 +2,7 @@
OpenMS -- Open-Source Mass Spectrometry
--------------------------------------------------------------------------
Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
ETH Zurich, and Freie Universitaet Berlin 2002-2013.
ETH Zurich, and Freie Universitaet Berlin 2002-2015.
This software is released under a three-clause BSD license:
* Redistributions of source code must retain the above copyright
......
OpenMS is released under a 3 clause BSD license.
The respective respective license file can be found in the LICENSE file
--------------------------------------------------------------------------
OpenMS -- Open-Source Mass Spectrometry
--------------------------------------------------------------------------
Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
ETH Zurich, and Freie Universitaet Berlin 2002-2015.
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.
The source code of OpenMS is available via our homepage http://www.OpenMS.de
OpenMS depends on third party libraries which are listed below.
The sourcecode of these libraries is available from their website or can be
The source code of these libraries is available from their website or can be
obtained via a "contrib" package, which specifically configures these libraries
for OpenMS and is available on our website.
The respective respective license files for the contrib libraries can be found
in the "contrib" package root directory or online.
The respective license files for the contrib libraries can be found
in the "contrib" package root directory or online (see below).
libSVM
- URL: http://www.csie.ntu.edu.tw/~cjlin/libsvm/
- License.libSVM.txt
GSL
- URL: http://www.gnu.org/software/gsl/
- License.gpl-2.0.txt
- URL: http://www.csie.ntu.edu.tw/~cjlin/libsvm/
- License available at http://www.csie.ntu.edu.tw/~cjlin/libsvm/COPYRIGHT
GLPK
- URL: http://www.gnu.org/s/glpk/
- License.gpl-3.0.txt
- URL: http://www.gnu.org/s/glpk/
- License available at http://www.gnu.org/copyleft/gpl.html
Qt 4
- URL: http://qt.nokia.com/
- License available at http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
- URL: http://qt.nokia.com/
- License available at http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
Xerces-C
- URL: http://xerces.apache.org/xerces-c/index.html
- License available at http://www.apache.org/licenses/LICENSE-2.0.html
- URL: http://xerces.apache.org/xerces-c/index.html
- License available at http://www.apache.org/licenses/LICENSE-2.0.html
Boost (headers)
- URL: http://www.boost.org/
- License available at http://www.boost.org/more/license_info.html
- URL: http://www.boost.org/
- License available at http://www.boost.org/more/license_info.html
ZLib
- URL: http://www.zlib.net
- License available at http://www.zlib.net/zlib_license.html
......@@ -56,3 +79,10 @@ MyriMatch:
- URL and source code: http://fenchurch.mc.vanderbilt.edu/software.php
- License available at: http://www.apache.org/licenses/LICENSE-2.0.txt
MSGF+:
- URL and source code: http://proteomics.ucsd.edu/Software/MSGFPlus/
- License available at: http://sourceforge.net/p/open-ms/code/HEAD/tree/THIRDPARTY/All/MSGFPlus/LICENSE.txt
Fido:
- URL and source code: https://noble.gs.washington.edu/proj/fido/
- License available at: https://gist.github.com/hendrikweisser/2d10eb8bf1e370e6dfbb
......@@ -7,22 +7,41 @@
This directory contains the source code of OpenMS.
License information can be found in the License.txt file.
If you downloaded a stable release, detailled installation
If you downloaded a stable release, detailed installation
instructions and other information can be found in the
documentation (doc/index.html).
If this is a development version obtained via SVN or as
nightly snapshot, the documentation is not contained in
this package. Please refer to the OpenMS website for
installation instructions then.
installation instructions.
------------------------------
-- TOPP tools --
------------------------------
In addition to the OpenMS library 'The OpenMS Proteomics
Pipeline' - TOPP is also included in this package.
Pipeline' (TOPP) is also included in this package.
The installation instructions for OpenMS also contain
installation instructions for TOPP!
------------------------------
-- Contributing --
------------------------------
If you would like to contribute to OpenMS, this is how
to best get started:
- Familiarize yourself with our online documentation,
available at http://www.openms.de/current_doxygen/html/
- Learn how to build OpenMS (by reading the building
instructions at the online documentation)
- Start reading the OpenMS tutorial for developers at
http://www.openms.de/current_doxygen/html/OpenMS_tutorial.html
- Any questions can be directed at the mailing list,
see http://openms.de/support for up-to-date information
about how to contact the OpenMS developers.
OpenMS
======
[![Build Status](https://travis-ci.org/OpenMS/OpenMS.svg?branch=develop)](https://travis-ci.org/OpenMS/OpenMS) [![Project Stats](https://www.ohloh.net/p/open-ms/widgets/project_thin_badge.gif)](https://www.ohloh.net/p/open-ms)
OpenMS is an open-source software C++ library for LC-MS data management and
analyses. It offers an infrastructure for the rapid development of mass
spectrometry related software. OpenMS is free software available under the
three clause BSD license and runs under Windows, MacOSX and Linux.
It comes with a vast variety of pre-built and ready-to-use tools for proteomics
and metabolomics data analysis (TOPPTools) and powerful 2D and 3D
visualization(TOPPView).
OpenMS offers analyses for various quantitation protocols, including label-free
quantitation, SILAC, iTRAQ, SRM, SWATH, etc.
It provides built-in algorithms for de-novo identification and database search,
as well as adapters to other state-of-the art tools like XTandem, Mascot,
OMSSA, etc. It supports easy integration of OpenMS built tools into workflow
engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and
a unified parameter handling via a 'common tool description' (CTD) scheme.
With PyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API
to enable rapid algorithm development. OpenMS supports the Proteomics Standard
Initiative (PSI) formats for MS data. The main contributors of OpenMS are
currently the Eberhard-Karls Universität in Tübingen, the Freie Universität
Berlin and the ETH Zurich.
Features
--------
- Core C++ library
- TOPP Tools, 150+ analysis tools (150+), covering most MS and LC-MS data processing and mining tasks.
- Support for all major platforms (Windows [XP, 7, 8], Linux, MacOS).
Licence
-------