diff --git a/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md b/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md index 7c16181f..47707d6e 100644 --- a/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md +++ b/docs/additional-resources/developer-guidelines-for-addding-new-dependent-libraries.md @@ -25,17 +25,17 @@ with e.g. LGPL-2 would be prohibitive. ## C++ standard compatibility -Needs to be compatible and therefore compilable with the same C++ standard as OpenMS. +New dependency libraries needs to be compatible and therefore compilable with the same C++ standard as OpenMS. ## Availability for all platforms -OpenMS is meant to run and behave the same on the three main operating systems, i.e., Windows, macOS and Linux. Adding -a new dependent library is thus required to be available on these platforms +OpenMS has been designed for Windows, macOS, and Linux. Therefore, the new dependency library needs to be designed for +these platforms. - on **WindowsOS** this usually means, adding the new library to the Contrib in debug and release variants. In short all recent versions of Visual Studio (VS2008 and onwards) must be supported (or support must be added). This encompasses - a solution file (which can be either statically present or generated by a meta-system like CMake) is available - - the lib actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will + - The library actually compiles and is linked to the **dynamic** VS-C++ runtime lib (since this is what the OpenMS lib will link to as well - combining static and dynamic links will lead to linker errors or segfaults). - on **macOS** it should be ensured that the library can be build on recent macOS versions (> 10.10) compiled using the diff --git a/docs/additional-resources/external-code-using-openms.md b/docs/additional-resources/external-code-using-openms.md index 5371faf8..fbdcb57f 100644 --- a/docs/additional-resources/external-code-using-openms.md +++ b/docs/additional-resources/external-code-using-openms.md @@ -103,7 +103,7 @@ If you've used an external project and have a new executable (+ an optional new well, and manually copy the new executable to the `TOPP/UTILS` binary directory (e.g. on Windows this could be `c:/program files/OpenMS/bin`, on Linux it could be `/bin`. -If you do NOT use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be +If you do not use the installer, copy all required files manually, plus a few extra steps, see below. What needs to be done is a little platform dependent, thus very cumbersome to explain. Look at the cmake installer scripts, to see whats required (for Mac and Linux see `OpenMS/cmake/package*.cmake`). diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md index b611400a..4e73e31b 100644 --- a/docs/guides/user-guides/user-quickstart-guide.md +++ b/docs/guides/user-guides/user-quickstart-guide.md @@ -31,7 +31,7 @@ Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOP Alternatively, use the command line and call tools directly. In this case, you'll probably want to use some type of shell script for automation. -## Adapte pipeline parameters +## Adapt pipeline parameters The default parameters of each tool can usually be tweaked to fit the data and improve results. diff --git a/docs/index.rst b/docs/index.rst index 740ae7a8..7d059105 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,7 +17,7 @@ quantitation, :term:`SILAC`, :term:`iTRAQ`, :term:`TMT`, :term:`SRM`, :term:`SWA 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, :term:`Mascot`, OMSSA, etc. It supports easy integration of OpenMS built tools into workflow -engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the TOPPtools concept and +engines like :term:`KNIME`, Galaxy, WS-Pgrade, and :term:`TOPPAS` via the :term:`TOPP tools` concept and a unified parameter handling via a 'common tool description' (CTD) scheme. With :term:`pyOpenMS`, OpenMS offers Python bindings to a large part of the :term:`OpenMS API` diff --git a/docs/tutorials/TOPP/TOPP-tutorial.md b/docs/tutorials/TOPP/TOPP-tutorial.md index 90aea6f2..10e6ec9b 100644 --- a/docs/tutorials/TOPP/TOPP-tutorial.md +++ b/docs/tutorials/TOPP/TOPP-tutorial.md @@ -1,15 +1,16 @@ TOPP Tutorial ============ -This tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and +The following tutorial is an introduction to {term}`TOPP` and {term}`TOPPView`. Let's start with understanding the intent and concept of {term}`TOPP` compared to OpenMS. Later, we will move to the handling of {term}`TOPPView` which is our central GUI. Apart from viewing data, {term}`TOPPView` can also be used to analyze it using selected {term}`TOPP tools`; how-to is explained in the third part of the tutorial. + Finally, the tutorial lists the command line interfaces for all TOPP tools contained in the release. # Concepts -Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md) in this part. +Let's understand the intent of [TOPP and OpenMS](topp-and-openms-introduction.md). ```{toctree} :maxdepth: 1 @@ -19,7 +20,7 @@ topp-and-openms-introduction # TOPPView Main Interface -In this part of the tutorial, we will learn about the main features of {term}`TOPPView` and its basic uses. +In the following section, we will learn about the main features of {term}`TOPPView` and its basic uses. ```{toctree} :maxdepth: 1 @@ -34,7 +35,7 @@ hotkeys-table # Calling TOPP tools from TOPPView -This part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from +The following part of the tutorial illustrates how to interactively analyse {term}`proteomics` data using {term}`TOPP tools` from within {term}`TOPPView`. ```{toctree} diff --git a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md index f44f47a7..b604804b 100644 --- a/docs/tutorials/TOPPAS/TOPPAS-tutorial.md +++ b/docs/tutorials/TOPPAS/TOPPAS-tutorial.md @@ -1,9 +1,9 @@ TOPPAS Tutorial ============== -**TOPPAS** allows to create, edit, open, save, and run TOPP workflows. Pipelines can be created conveniently in a GUI. -The parameters of all involved tools can be edited within TOPPAS and are also saved as part of the pipeline definition - in the `.toppas` file. +**TOPPAS** is a GUI tool that is used to create, edit, open, save, and run TOPP workflows. Pipelines can be created +conveniently in a GUI. The parameters of all involved tools can be edited within TOPPAS and are also saved as part of +the pipeline definition in the `.toppas` file. ```{toctree} :maxdepth: 1 diff --git a/docs/tutorials/TOPPAS/examples.md b/docs/tutorials/TOPPAS/examples.md index 9d42c732..ecec532d 100644 --- a/docs/tutorials/TOPPAS/examples.md +++ b/docs/tutorials/TOPPAS/examples.md @@ -17,8 +17,8 @@ TOPPView tutorial: [Smoothing raw data](../TOPP/smoothing-raw-data.md), [Subtrac ## Identification of E. coli peptides This section describes an example identification pipeline contained in the example directory, `Ecoli_Identification.toppas`. -It is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an Orbitrap -instrument as well as an E. coli target-decoy database. +The pipeline is shipped together with a reduced example mzML file containing 139 MS2 spectra from an E. coli run on an +Orbitrap instrument as well as an E. coli target-decoy database. Use the search engine OMSSA (Geer et al., 2004) for peptide identification. Therefore, OMSSA must be installed and the path to the OMSSA executable (omssacl) must be set in the parameters of the OMSSAAdapter node.