From 2af8b38b834c095711fd046773f476a0c442f957 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Tue, 7 Jun 2022 21:16:54 +0530
Subject: [PATCH 01/14] Address review comments by @greengypsy

Ref: https://github.com/OpenMS/OpenMS-docs/pull/65.
---
 ...per-guidelines-for-addding-new-dependent-libraries.md | 8 ++++----
 docs/additional-resources/external-code-using-openms.md  | 2 +-
 docs/guides/user-guides/user-quickstart-guide.md         | 2 +-
 docs/index.rst                                           | 2 +-
 docs/tutorials/TOPP/TOPP-tutorial.md                     | 9 +++++----
 docs/tutorials/TOPPAS/TOPPAS-tutorial.md                 | 6 +++---
 docs/tutorials/TOPPAS/examples.md                        | 4 ++--
 7 files changed, 17 insertions(+), 16 deletions(-)

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.

From f17e6f8f62f52e65380c98fc95198d016a4020c3 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Wed, 8 Jun 2022 16:30:11 +0530
Subject: [PATCH 02/14] add: exact syntax for adding admonition

---
 .github/CONTRIBUTING.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index ff30302a..90a7699e 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -31,7 +31,7 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op
 6. Use `backtick`(s) for formatting code, library name, files, and path.
 7. Use **bold** for product name, object name, an independent entity.
 8. Use **bold** for menu title in an application.
-9. Link to glossary terms using {term}`this is a glossary term`.
+9. Link to glossary terms using {term}\`this is a glossary term\`.
 10. OpenMS documentation uses following Admonitions
     - Hint
 	- Important
@@ -39,6 +39,7 @@ For any questions, drop us a ping in [OpenMS Gitter](https://gitter.im/OpenMS/Op
 	- Warning
 	- Tip
 	- See Also
+
 	Example of these are present in documentation, please follow them.
 11. Always specify lexers for code blocks.
 12. Format keyboard strokes using `<kbd>qwerty-keyboard-button</kbd>`, as an example, please see [this](../docs/tutorials/TOPP/hotkeys-table.md) file.

From 509a43be688005cc91cfd930eee47275e493bfde Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Wed, 8 Jun 2022 16:37:26 +0530
Subject: [PATCH 03/14] add: soon to be deprecated important admonition for
 toppas

---
 docs/guides/user-guides/user-quickstart-guide.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md
index 4e73e31b..acbfd1cb 100644
--- a/docs/guides/user-guides/user-quickstart-guide.md
+++ b/docs/guides/user-guides/user-quickstart-guide.md
@@ -22,6 +22,12 @@ Before using OpenMS, become familiar with the following terms:
 |**TOPP tools**      |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)|
 |**UTILS**           |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)|
 
+```{important}
+Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future.
+Please find more information about using {term}`KNIME` in [KNIME tutorial](../../tutorials/KNIME/KNIME-tutorial.md).
+```
+
+
 ## How to run a Tool
 
 A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`).

From e167563e9040bd0642b2d7a4f0a4cc2d424535ba Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Fri, 10 Jun 2022 17:55:52 +0530
Subject: [PATCH 04/14] add: remaining toppview-introduction content

Closes https://github.com/OpenMS/OpenMS-docs/issues/76.
---
 docs/images/tutorials/topp/TOPPView_help.png | Bin 0 -> 18850 bytes
 docs/tutorials/TOPP/toppview-introduction.md |  72 +++++++++++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 docs/images/tutorials/topp/TOPPView_help.png

diff --git a/docs/images/tutorials/topp/TOPPView_help.png b/docs/images/tutorials/topp/TOPPView_help.png
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diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md
index 7ac5e984..9a266acf 100644
--- a/docs/tutorials/TOPP/toppview-introduction.md
+++ b/docs/tutorials/TOPP/toppview-introduction.md
@@ -11,3 +11,75 @@ datasets as well as displaying input data and output data of an algorithm togeth
 developers.
 
 ![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png)
+
+The above example image shows a 2D view of TOPPView (blue rectangle) and the corresponding [Display modes and view options](display-modes-and-view-options.md) (red rectangle). The right dock area, shows the [Layers](#layers) (yellow rectangle), the [Spectrum browser](#spectrum-browser) (magenta rectangle) and the [Data filtering](data-filtering) (green rectangle). Switch between open windows can
+be done using the tab bar (black rectangle).
+
+## Layers
+
+Each view of TOPPView supports several datasets, called layers. In the *layer manager* (dock window in the upper right
+corner), layers can be hidden and shown using the check box in front of each layer name.
+
+By clicking on a layer, this layer is selected, which is indicated by a blue background. The selected layer can be
+manipulated using the *Tools* menu.
+
+Layers can be copied by dragging them to the tab bar. If the layer is dropped on a tab, it is added to the corresponding
+window. If the layer is dropped on the tab bar but not on a tab, a new window with that layer is added.
+
+## Spectrum browser
+
+The spectra contained in a peak map can be browsed in the *spectrum browser*. It displays a tree view of all spectra in
+the current layer, where a spectrum with MS level *n* is a child of the spectrum with MS level *n - 1* that contains its
+corresponding precursor peak. For each spectrum in the list, the retention time and (for spectra with MS level > 1) the
+m/z value of the precursor peak are also shown.
+
+If a 2D or 3D window is active, double-clicking a spectrum will open it in a new 1D window. If the active window is a 1D
+view, the spectra can be browsed and the currently selected spectrum will be shown.
+
+## Data filtering
+
+TOPPView allows filtering of the displayed peak data and feature data. Peak data can be filtered according to intensity
+and meta data. Meta data is arbitrary data the peak is annotated with. Feature data can be filtered according to
+intensity, charge, quality and meta data.
+
+Data filters are managed by a dock window. Filters can be added, removed and edited through the context menu (right
+button mouse click) of the data filters window. For convenience, filters can also be edited by double-clicking them.
+
+## Command line options
+
+Several files can be opened in one layer from the command line by putting a '+' character between the file names. The
+following command opens three files in three layers of the same window:
+
+```bash
+TOPPView file1.mzML + file2.mzML + file3.mzML
+```
+
+Without the '+' the files would be opened in three different tabs.
+
+The color gradient used to display a file can be changed by adding one of several '@' commands. The following command
+opens the file with a white-to-black gradient:
+
+```bash
+TOPPView file1.mzML @bw
+```
+
+Automatic annotation of a layer with ID data (.osw files etc) can be performed by using the '!' character. This will
+treat the next filename as annotation to the previous layer. The following command opens two layers in the same tab,
+with the first layer being annotated:
+
+```bash
+TOPPView file1.mzML ! file1.idXML + file2.mzML
+```
+
+For more information on command line parameters call:
+
+```bash
+TOPPView --help
+```
+
+## Looking for help?
+
+You can display a short help text for each button and dock window of TOPPView by clicking on it in *What's this?* mode.
+*What's this?* mode can be entered using the *Help* menu.
+
+![](../../images/tutorials/topp/TOPPView_help.png)

From 025faeaa831b2c8510bc9011e4754458fc69f27c Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Fri, 10 Jun 2022 17:56:12 +0530
Subject: [PATCH 05/14] prettier: ui enhancements

Fixes https://github.com/OpenMS/OpenMS-docs/issues/66.
Fixes https://github.com/OpenMS/OpenMS-docs/issues/71.
Closes https://github.com/OpenMS/OpenMS-docs/issues/79.
Fixes https://github.com/OpenMS/OpenMS-docs/issues/81.
---
 conf.py                                       | 10 ++++
 docs/contact-us.md                            |  2 +-
 docs/glossary.md                              |  3 --
 .../user-guides/user-quickstart-guide.md      | 13 +++--
 docs/index.rst                                |  4 +-
 .../installation-on-gnu-linux.md              | 44 +++++++++--------
 docs/introduction.md                          | 13 +++++
 .../adding-new-tool-to-topp.md                |  0
 .../ini-file-editor.md                        |  0
 docs/topp-and-utils/proteomicslfq.md          | 49 +++++++++++++++++++
 docs/{topp => topp-and-utils}/swathwizard.md  |  0
 .../topp-and-utils.md}                        | 24 ++++++++-
 docs/{topp => topp-and-utils}/toppas.md       |  0
 docs/{topp => topp-and-utils}/toppview.md     |  0
 .../TOPP/display-modes-and-view-options.md    |  4 +-
 .../TOPP/peptide-property-prediction.md       |  2 +-
 docs/tutorials/TOPP/picking-peaks.md          |  2 +-
 .../tutorials/TOPP/profile-data-processing.md |  4 +-
 18 files changed, 136 insertions(+), 38 deletions(-)
 rename docs/{topp => topp-and-utils}/adding-new-tool-to-topp.md (100%)
 rename docs/{topp => topp-and-utils}/ini-file-editor.md (100%)
 create mode 100644 docs/topp-and-utils/proteomicslfq.md
 rename docs/{topp => topp-and-utils}/swathwizard.md (100%)
 rename docs/{topp/topp.md => topp-and-utils/topp-and-utils.md} (61%)
 rename docs/{topp => topp-and-utils}/toppas.md (100%)
 rename docs/{topp => topp-and-utils}/toppview.md (100%)

diff --git a/conf.py b/conf.py
index 0524eee0..e7f0afde 100644
--- a/conf.py
+++ b/conf.py
@@ -36,6 +36,16 @@
   'sphinx_inline_tabs',
 ]
 
+myst_enable_extensions = [
+  "tasklist",
+  "dollarmath",
+  "amsmath",
+  "colon_fence",
+  "linkify",
+  "replacements",
+  "linkify_fuzzy_links",
+]
+
 autosummary_generate = True
 autosummary_imported_members = True
 
diff --git a/docs/contact-us.md b/docs/contact-us.md
index 3f450fd3..6d3cc82c 100644
--- a/docs/contact-us.md
+++ b/docs/contact-us.md
@@ -1,7 +1,7 @@
 Contact Us
 =========
 
-Join us on [Discord](https://discord.com/invite/swkxs72CHB)!
+Join us on [Discord](https://discord.gg/WxynEEsf5X)!
 
 You can also contact us:
 
diff --git a/docs/glossary.md b/docs/glossary.md
index e3f2eb48..764ae707 100644
--- a/docs/glossary.md
+++ b/docs/glossary.md
@@ -102,9 +102,6 @@ Collision-induced dissociation (CID)
 TOPP
   The OpenMS Proteomics Pipeline.
 
-TOPPAS.app
-  TOPPAS allows to create, edit, open, save, and run TOPP workflows.
-
 MSGFPlusAdapter
   Adapter for the MS-GF+ protein identification (database search) engine. More information is available [here](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_MSGFPlusAdapter.html).
 
diff --git a/docs/guides/user-guides/user-quickstart-guide.md b/docs/guides/user-guides/user-quickstart-guide.md
index 5293ab1b..71d07e42 100644
--- a/docs/guides/user-guides/user-quickstart-guide.md
+++ b/docs/guides/user-guides/user-quickstart-guide.md
@@ -19,8 +19,13 @@ Before using OpenMS, become familiar with the following terms:
 |--------------------|-------------|
 |**TOPPView**        |A tool that is used to view and explore {term}`LC-MS` data, alignments, groups, peptide identifications, and more.|
 |**TOPPAS**          |A graphical workflow design tool that is used to create pipelines from all {term}`TOPP tools` (and {term}`UTILS`).|
-|**TOPP tools**      |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp/topp.md)|
-|**UTILS**           |Similar to {term}`TOPP tools`, but with more supporting character, which are rarely used in a productive pipeline, but rather during pipeline construction or parameter optimization. See also: [UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)|
+|**TOPP tools**      |A set of command line tools. Each of these command line tools is a building block of an analysis pipeline and are chained together in a way that fits the requirements of the user. The {term}`TOPP tools` are accessible from a command prompt/shell or via {term}`TOPPAS`. See also: [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md) and [TOPP documentation](../../topp-and-utils/topp-and-utils.md)|
+|**UTILS**           |Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline construction or parameter optimization. |
+
+```{seealso}
+
+[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)|
+```
 
 ```{important}
 Users can now use {term}`KNIME` in place of {term}`TOPPAS`; the later will deprecated with no support in near future.
@@ -32,7 +37,7 @@ Please find more information about using {term}`KNIME` in [KNIME tutorial](../..
 
 A good start are the example pipelines (select **File** > **Open example file** within {term}`TOPPAS`).
 
-Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp/topp.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)).
+Read the documentation of the tools see [TOPP tutorial](../../tutorials/TOPP/TOPP-tutorial.md), [TOPP documentation](../../topp-and-utils/topp-and-utils.md) and the one of ([TOPPAS tutorial](../../tutorials/TOPPAS/TOPPAS-tutorial.md)).
 
 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.
@@ -54,7 +59,7 @@ The default parameters of each tool can usually be tweaked to fit the data and i
 
    e.g. `FileFilter -write_ini filefilter.ini`
 
-   Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp/ini-file-editor.md), which is another GUI tool shipped with
+   Now, edit the INI file (which is a XML file) using the [INIFileEditor](../../topp-and-utils/ini-file-editor.md), which is another GUI tool shipped with
    OpenMS and similar to the one build into {term}`TOPPAS`.
 
 ### How do I feed the INI file to a Tool?
diff --git a/docs/index.rst b/docs/index.rst
index eb92fa7a..60195449 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -71,8 +71,8 @@ Contents
    :maxdepth: 2
    :caption: OpenMS TOPP Tools
 
-   topp/topp.md
-   topp/adding-new-tool-to-topp.md
+   topp-and-utils/topp-and-utils.md
+   topp-and-utils/adding-new-tool-to-topp.md
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
index f6482b31..0da62ce9 100644
--- a/docs/installations/installation-on-gnu-linux.md
+++ b/docs/installations/installation-on-gnu-linux.md
@@ -5,16 +5,6 @@ Installation on GNU/Linux
 
 Use conda or bioconda to install OpenMS.
 
-1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
-2. Install OpenMS using conda:
-   `conda install -c openms openms`
-3. Other OpenMS packages can be installed using:
-   ```
-   conda install -c openms pyopenms
-   conda install -c openms openms-thirdparty
-   conda install -c openms libopenms
-   ```
-
 ```{tab} openms
 openms contains OpenMS C++ Tools.
 ```
@@ -32,6 +22,16 @@ openms-thirdparty are external tools that are wrapped in OpenMS with adapters. T
 the openms package.
 ```
 
+1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
+2. Install OpenMS using conda:
+   `conda install -c openms openms`
+3. Other OpenMS packages can be installed using:
+   ```
+   conda install -c openms pyopenms
+   conda install -c openms openms-thirdparty
+   conda install -c openms libopenms
+   ```
+
 To install using bioconda:
 
 ```
@@ -85,13 +85,8 @@ These packages are not directly maintained by the OpenMS team and they can not b
 same behaviour as when building it from source code. Also, their availability and version is subject to change and
 support might be limited (due to unforeseen or untested behaviour). It is suggested not to install them parallel to our
 Debian package.
-
 ```
 
-## Installation via building from source code
-
-The source code of OpenMS is available on GitHub. Follow [Building OpenMS on GNU/Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/install_linux.html) instructions on how to build OpenMS from source.
-
 ```{note}
 Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
 ```
@@ -102,8 +97,17 @@ Make sure you have [Docker installed](https://docs.docker.com/engine/install/).
 
 Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io).
 
-1. [openms-executables](https://ghcr.io/openms/openms-executables:latest)
-2. [openms-library](https://ghcr.io/openms/openms-library:latest)
+```{tab}
+
+[openms-executables](https://ghcr.io/openms/openms-executables:latest)
+
+```
+
+```{tab}
+
+[openms-library](https://ghcr.io/openms/openms-library:latest)
+
+```
 
 Or via [BioContainers Registeries](https://biocontainers.pro/registry).
 
@@ -116,9 +120,9 @@ Docker images can be pulled via or one of the following commands:
 
 ```
 docker pull biocontainers/openms
-docker pull openms/library
-docker pull openms/executables
-docker pull openms/pyopenms
+docker pull biocontainers/libopenms
+docker pull biocontainers/openms-thirdparty
+docker pull biocontainers/pyopenms
 ```
 
 Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on
diff --git a/docs/introduction.md b/docs/introduction.md
index 324089e2..c8d6ef45 100644
--- a/docs/introduction.md
+++ b/docs/introduction.md
@@ -94,13 +94,26 @@ Get started with installing OpenMS using the installers available for different
 ## Installation on different platforms
 
 ```{tab} GNU/Linux
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Debian-Linux-x86_64.deb
+
+```
+
 ```
 
 ```{tab} Windows
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-Win64.exe
 ```
 
+```
+
 ```{tab} macOS
+
+```bash
 wget https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/OpenMS-2.8.0-macOS.dmg
 ```
+
+```
diff --git a/docs/topp/adding-new-tool-to-topp.md b/docs/topp-and-utils/adding-new-tool-to-topp.md
similarity index 100%
rename from docs/topp/adding-new-tool-to-topp.md
rename to docs/topp-and-utils/adding-new-tool-to-topp.md
diff --git a/docs/topp/ini-file-editor.md b/docs/topp-and-utils/ini-file-editor.md
similarity index 100%
rename from docs/topp/ini-file-editor.md
rename to docs/topp-and-utils/ini-file-editor.md
diff --git a/docs/topp-and-utils/proteomicslfq.md b/docs/topp-and-utils/proteomicslfq.md
new file mode 100644
index 00000000..55bd1122
--- /dev/null
+++ b/docs/topp-and-utils/proteomicslfq.md
@@ -0,0 +1,49 @@
+ProteomicsLFQ
+=============
+
+
+ProteomicsLFQ performs label-free quantification of peptides and proteins.
+
+## Input
+
+- Spectra in mzML format
+- Identifications in idXML or mzIdentML format with posterior error probabilities as score type. To generate those we
+  suggest to run:
+  - PeptideIndexer to annotate target and decoy information.
+  - PSMFeatureExtractor to annotate percolator features.
+  - PercolatorAdapter tool (score_type = 'q-value', -post-processing-tdc).
+  - IDFilter (pep:score = 0.01) to filter PSMs at 1% FDR.
+- An experimental design file:
+
+  ```{seealso}
+  [Experimental Design](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ExperimentalDesign.html) for details.
+  ```
+- A protein database in with appended decoy sequences in FASTA format.
+  (e.g., generated by the [OpenMS DecoyDatabase tool](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/namespaceOpenMS.html)).
+  Processing:
+  ProteomicsLFQ has different methods to extract features: ID-based (targeted only), or both ID-based and untargeted.
+  -  The first method uses targeted feature dectection using RT and m/z information derived from identification data to
+     extract features.
+	 ```{note}
+	 Only identifications found in a particular MS run are used to extract features in the same run. No transfer of IDs
+	 (match between runs) is performed.
+	 ```
+  - The second method adds untargeted feature detection to obtain quantities from unidentified features. Transfer of Ids
+    (match between runs) is performed by transfering feature identifications to coeluting, unidentified features with
+	similar mass and RT in other runs.
+
+## Requantification
+
+Optionally, a requantification step is performed that tries to fill NA values. If a peptide has been quantified in
+more than half of all maps, the peptide is selected for requantification. In that case, the mean observed RT
+(and theoretical m/z) of the peptide is used to perform a second round of targeted extraction.
+
+## Output
+
+Output format are as follows:
+
+- mzTab file with analysis results.
+- MSstats file with analysis results for statistical downstream analysis in MSstats.
+- ConsensusXML file for visualization and further processing in OpenMS.
+
+Potential scripts to perform the search can be found under `src/tests/topp/ProteomicsLFQTestScripts`.
diff --git a/docs/topp/swathwizard.md b/docs/topp-and-utils/swathwizard.md
similarity index 100%
rename from docs/topp/swathwizard.md
rename to docs/topp-and-utils/swathwizard.md
diff --git a/docs/topp/topp.md b/docs/topp-and-utils/topp-and-utils.md
similarity index 61%
rename from docs/topp/topp.md
rename to docs/topp-and-utils/topp-and-utils.md
index 7309d620..23f0d78e 100644
--- a/docs/topp/topp.md
+++ b/docs/topp-and-utils/topp-and-utils.md
@@ -1,5 +1,5 @@
 TOPP
-===
+====
 
 **TOPP - The OpenMS Proteomics Pipeline** is a pipeline for the analysis of HPLC-MS data. It consists of several small
 applications that can be chained to create analysis pipelines tailored for a specific problem.
@@ -20,3 +20,25 @@ swathwizard
 ```
 
 For advanced documentation on every TOPP tool, see the [OpenMS TOPP API Reference](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_documentation.html).
+
+UTILS
+=====
+
+Besides {term}`TOPP`, OpenMS offers range of other tools. They are not included in {term}`TOPP` as they are not part of
+typical analysis pipelines. A set of command line utilities, similar to {term}`TOPP tools`, mostly used during pipeline
+construction or parameter optimization.
+
+
+```{seealso}
+
+[UTILS documentation](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_documentation.html)
+
+```
+
+Let's explore one such utitliy tool:
+
+```{toctree}
+:maxdepth: 1
+
+proteomicslfq
+```
diff --git a/docs/topp/toppas.md b/docs/topp-and-utils/toppas.md
similarity index 100%
rename from docs/topp/toppas.md
rename to docs/topp-and-utils/toppas.md
diff --git a/docs/topp/toppview.md b/docs/topp-and-utils/toppview.md
similarity index 100%
rename from docs/topp/toppview.md
rename to docs/topp-and-utils/toppview.md
diff --git a/docs/tutorials/TOPP/display-modes-and-view-options.md b/docs/tutorials/TOPP/display-modes-and-view-options.md
index 503d3c41..75b4eac6 100644
--- a/docs/tutorials/TOPP/display-modes-and-view-options.md
+++ b/docs/tutorials/TOPP/display-modes-and-view-options.md
@@ -6,7 +6,7 @@ Display modes determine how intensities are displayed. View options configure th
 
 ![TOPPView Icons](../../images/tutorials/topp/TOPPView_icons.png)
 
-# Display Modes
+## Display Modes
 
 Intensity display modes determine the way peak intensities are displayed.
 
@@ -24,7 +24,7 @@ opened it corresponds to the normal mode.
 
 In this mode the maximum currently displayed intensity is treated as if it was the maximum overall intensity.
 
-# View Options
+## View Options
 
 View options configure the view of the current layer.
 
diff --git a/docs/tutorials/TOPP/peptide-property-prediction.md b/docs/tutorials/TOPP/peptide-property-prediction.md
index 1406e81f..c46ec173 100644
--- a/docs/tutorials/TOPP/peptide-property-prediction.md
+++ b/docs/tutorials/TOPP/peptide-property-prediction.md
@@ -1,7 +1,7 @@
 Peptide Property Prediction
 ===========================
 
-You can train a model for retention time prediction as well as for the prediction of proteotypic peptides.
+Train a model for retention time prediction as well as for the prediction of proteotypic peptides.
 
 Two applications has been described in the following publications: Nico Pfeifer, Andreas Leinenbach, Christian G. Huber
 and Oliver Kohlbacher Statistical learning of peptide retention behavior in chromatographic separations: A new
diff --git a/docs/tutorials/TOPP/picking-peaks.md b/docs/tutorials/TOPP/picking-peaks.md
index b31845b4..8a00b905 100644
--- a/docs/tutorials/TOPP/picking-peaks.md
+++ b/docs/tutorials/TOPP/picking-peaks.md
@@ -13,7 +13,7 @@ the approximate `fwhm` of peaks, use the estimation included in the PeakPickerWa
 to `true`. After applying the PeakPickerWavelet, observe which peak width was estimated and used for peak picking in the
 log window.
 
-To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md##action-modes-and-their-uses)) to determine
+To estimate the peak width, use the measuring tool ([Action Modes and Their Uses](views-in-toppview.md#action-modes-and-their-uses)) to determine
 the fwhm of one or several representative peaks.
 
 If the peak picker delivers only a few peaks even though the `peak_with` and `signal_to_noise` parameters are set to
diff --git a/docs/tutorials/TOPP/profile-data-processing.md b/docs/tutorials/TOPP/profile-data-processing.md
index 55340593..7c45c122 100644
--- a/docs/tutorials/TOPP/profile-data-processing.md
+++ b/docs/tutorials/TOPP/profile-data-processing.md
@@ -51,9 +51,7 @@ Please notice that this method is still **experimental** since it has not been t
 
   See the `PeakPickerHiRes` class documentation for a parameter list.
 
-## Finding the right parameters for the
-
-NoiseFilters, the BaselineFilter and the PeakPickers
+## Finding the right parameters for the NoiseFilters, the BaselineFilter and the PeakPickers
 
 Finding the right parameters is not trivial. The default parameters will not work on most datasets. In order to find
 good parameters, following this procedure:

From a940f0a59e56710881478fe239e674eaf02670c5 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Fri, 10 Jun 2022 17:53:34 +0530
Subject: [PATCH 06/14] fixes: merge conflicts

---
 docs/tutorials/TOPP/toppview-introduction.md | 85 --------------------
 1 file changed, 85 deletions(-)
 delete mode 100644 docs/tutorials/TOPP/toppview-introduction.md

diff --git a/docs/tutorials/TOPP/toppview-introduction.md b/docs/tutorials/TOPP/toppview-introduction.md
deleted file mode 100644
index 9a266acf..00000000
--- a/docs/tutorials/TOPP/toppview-introduction.md
+++ /dev/null
@@ -1,85 +0,0 @@
-TOPPView Introduction
-=====================
-
-{term}`TOPPView` is a viewer for {term}`MS` and {term}`HPLC-MS` data. It can be used to inspect files in {term}`mzML`,
-{term}`mzData`, {term}`mzXML` and several other text-based file formats.
-
-In each view, several datasets can be displayed using the layer concept. This allows visual comparison of several
-datasets as well as displaying input data and output data of an algorithm together.
-
-{term}`TOPPView` is intended for visual inspection of the data by experimentalists as well as for analysis software by
-developers.
-
-![TOPPView Parts](../../images/tutorials/topp/TOPPView_parts.png)
-
-The above example image shows a 2D view of TOPPView (blue rectangle) and the corresponding [Display modes and view options](display-modes-and-view-options.md) (red rectangle). The right dock area, shows the [Layers](#layers) (yellow rectangle), the [Spectrum browser](#spectrum-browser) (magenta rectangle) and the [Data filtering](data-filtering) (green rectangle). Switch between open windows can
-be done using the tab bar (black rectangle).
-
-## Layers
-
-Each view of TOPPView supports several datasets, called layers. In the *layer manager* (dock window in the upper right
-corner), layers can be hidden and shown using the check box in front of each layer name.
-
-By clicking on a layer, this layer is selected, which is indicated by a blue background. The selected layer can be
-manipulated using the *Tools* menu.
-
-Layers can be copied by dragging them to the tab bar. If the layer is dropped on a tab, it is added to the corresponding
-window. If the layer is dropped on the tab bar but not on a tab, a new window with that layer is added.
-
-## Spectrum browser
-
-The spectra contained in a peak map can be browsed in the *spectrum browser*. It displays a tree view of all spectra in
-the current layer, where a spectrum with MS level *n* is a child of the spectrum with MS level *n - 1* that contains its
-corresponding precursor peak. For each spectrum in the list, the retention time and (for spectra with MS level > 1) the
-m/z value of the precursor peak are also shown.
-
-If a 2D or 3D window is active, double-clicking a spectrum will open it in a new 1D window. If the active window is a 1D
-view, the spectra can be browsed and the currently selected spectrum will be shown.
-
-## Data filtering
-
-TOPPView allows filtering of the displayed peak data and feature data. Peak data can be filtered according to intensity
-and meta data. Meta data is arbitrary data the peak is annotated with. Feature data can be filtered according to
-intensity, charge, quality and meta data.
-
-Data filters are managed by a dock window. Filters can be added, removed and edited through the context menu (right
-button mouse click) of the data filters window. For convenience, filters can also be edited by double-clicking them.
-
-## Command line options
-
-Several files can be opened in one layer from the command line by putting a '+' character between the file names. The
-following command opens three files in three layers of the same window:
-
-```bash
-TOPPView file1.mzML + file2.mzML + file3.mzML
-```
-
-Without the '+' the files would be opened in three different tabs.
-
-The color gradient used to display a file can be changed by adding one of several '@' commands. The following command
-opens the file with a white-to-black gradient:
-
-```bash
-TOPPView file1.mzML @bw
-```
-
-Automatic annotation of a layer with ID data (.osw files etc) can be performed by using the '!' character. This will
-treat the next filename as annotation to the previous layer. The following command opens two layers in the same tab,
-with the first layer being annotated:
-
-```bash
-TOPPView file1.mzML ! file1.idXML + file2.mzML
-```
-
-For more information on command line parameters call:
-
-```bash
-TOPPView --help
-```
-
-## Looking for help?
-
-You can display a short help text for each button and dock window of TOPPView by clicking on it in *What's this?* mode.
-*What's this?* mode can be entered using the *Help* menu.
-
-![](../../images/tutorials/topp/TOPPView_help.png)

From 2c0f172202a35a5f7fb2d5c20b25913311777620 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:00 +0530
Subject: [PATCH 07/14] Revert "Try adding autosection"

This reverts commit e1f5b66fe28d895cf7e48f5f548f09076ca38b4b.
---
 conf.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf.py b/conf.py
index d69c157b..97f4ccbc 100644
--- a/conf.py
+++ b/conf.py
@@ -30,7 +30,6 @@
   'sphinx_copybutton',
   'sphinx.ext.autodoc',
   'sphinx.ext.autosummary',
-  'sphinx.ext.autosectionlabel',
   'myst_parser',
   'notfound.extension',
   'sphinxcontrib.images',

From fea35343a12719360e7397f69e8e6dcf3876bf33 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:07 +0530
Subject: [PATCH 08/14] Revert "try different link syntax"

This reverts commit 940fbdf84cfeb83e60cef1b064868881fed685c0.
---
 docs/installations/installation-on-macos.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md
index 48b5c61e..14a35775 100644
--- a/docs/installations/installation-on-macos.md
+++ b/docs/installations/installation-on-macos.md
@@ -39,7 +39,7 @@ Make sure `<OpenMS-PATH>` points to the folder where OpenMS is installed locally
 
 ## Install via Conda with the Bioconda channel
 
-Follow the instructions for {ref}`GNU/Linux <./installation-on-gnu-linux.md#install-via-conda>`. Use the Terminal.app or any
+Follow the instructions for [GNU/Linux](./installation-on-gnu-linux.md#install-via-conda). Use the Terminal.app or any
 terminal of your choice to run the commands.
 
 ```{note}
@@ -49,7 +49,7 @@ builds for macOS on our own conda channel `openms`.
 
 ## Run via (Bio)Container
 
-Follow the instructions for{ref}`GNU/Linux <./installation-on-gnu-linux.md#run-via-a-bio-container>`. Make sure to
+Follow the instructions for [GNU/Linux](./installation-on-gnu-linux.md#run-via-a-bio-container). Make sure to
 follow specific installation instructions for macOS during the installation of the containerization software.
 Use the Terminal.app or any terminal of your choice to run the commands.
 

From 75cd3c09934eef9e5e1d748b537fcf8acd19bd5f Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:14 +0530
Subject: [PATCH 09/14] Revert "Update conda instructions for macOS"

This reverts commit 4e7cf57b0cb753de361692aff2887ad1e5263b41.
---
 docs/installations/installation-on-macos.md | 22 ++-------------------
 1 file changed, 2 insertions(+), 20 deletions(-)

diff --git a/docs/installations/installation-on-macos.md b/docs/installations/installation-on-macos.md
index 14a35775..4e1769c3 100644
--- a/docs/installations/installation-on-macos.md
+++ b/docs/installations/installation-on-macos.md
@@ -37,27 +37,9 @@ source ${OPENMS_TOPP_PATH}/.TOPP_bash_profile
 
 Make sure `<OpenMS-PATH>` points to the folder where OpenMS is installed locally (e.g., `/Applications/OpenMS-<version>`)
 
-## Install via Conda with the Bioconda channel
+## Install via Conda or Bioconda
 
-Follow the instructions for [GNU/Linux](./installation-on-gnu-linux.md#install-via-conda). Use the Terminal.app or any
-terminal of your choice to run the commands.
-
-```{note}
-Due to unavailability of an exact copy of the macOS build machines used in bioconda, we currently cannot offer nightly
-builds for macOS on our own conda channel `openms`.
-```
-
-## Run via (Bio)Container
-
-Follow the instructions for [GNU/Linux](./installation-on-gnu-linux.md#run-via-a-bio-container). Make sure to
-follow specific installation instructions for macOS during the installation of the containerization software.
-Use the Terminal.app or any terminal of your choice to run the commands.
-
-```{note}
-Running OpenMS containers (currently built for Linux) on macOS involves
-running virtual machines (sometimes hidden from the user, e.g., with Docker).
-This comes with disadvantages in runtime and memory consumption.
-```
+Follow [these](installation-on-gnu-linux.md#install-via-conda) instructions.
 
 
 ## Build OpenMS from source

From a1a7f695e9e3d1908972cad24f9ab478c87538c6 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:29 +0530
Subject: [PATCH 10/14] Revert "[FIX] allow crosslinking in markdown"

This reverts commit 0241aa2c1c9e4ffd754ab0a6dea7ffd98967c15a.
---
 conf.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conf.py b/conf.py
index 97f4ccbc..1fd961a6 100644
--- a/conf.py
+++ b/conf.py
@@ -46,9 +46,6 @@
   "linkify_fuzzy_links",
 ]
 
-# Generate header anchors for cross-linking in markdown until depth n
-myst_heading_anchors = 3
-
 autosummary_generate = True
 autosummary_imported_members = True
 

From 8a8cb201de1d4f40b355405234c2037cd7bde18f Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:38 +0530
Subject: [PATCH 11/14] Revert "whitespace"

This reverts commit 83540a0dac5770924a52c7e13e09be8394bfa0aa.
---
 docs/installations/installation-on-gnu-linux.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
index f6c69fff..cd90a51a 100644
--- a/docs/installations/installation-on-gnu-linux.md
+++ b/docs/installations/installation-on-gnu-linux.md
@@ -164,7 +164,7 @@ docker pull quay.io/biocontainers/openms-thirdparty
 ```
 ````
 
-````{tab} Singularity
+````{tab}Singularity
 ```bash
 docker pull https://depot.galaxyproject.org/singularity/libopenms
 docker pull https://depot.galaxyproject.org/singularity/openms

From dbe234532059b1afb6efc6a778c18ff75e34efff Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:23:43 +0530
Subject: [PATCH 12/14] Revert "Fixes to tabbing"

This reverts commit b46d1124b91f521187ac3d9e9c4fdae91966603f.
---
 .../installation-on-gnu-linux.md              | 49 ++++++-------------
 1 file changed, 14 insertions(+), 35 deletions(-)

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
index cd90a51a..4ba01965 100644
--- a/docs/installations/installation-on-gnu-linux.md
+++ b/docs/installations/installation-on-gnu-linux.md
@@ -15,74 +15,58 @@ obtain release versions (`bioconda` channel) and nightly versions (`openms` chan
    ```
 3. Install any of the following packages related to OpenMS
 
-```{tab} openms
+```{group-tab} openms
 openms contains OpenMS C++ Tools.
 ```
 
-```{tab} libopenms
+```{group-tab} libopenms
 libopenms is the C++ library required for the OpenMS C++ Tools to work.
 ```
 
-```{tab} pyopenms
+```{group-tab} pyopenms
 pyopenms is the python package that allows to use algorithms from libopenms in Python.
 ```
 
-```{tab} openms-thirdparty
+```{group-tab} openms-thirdparty
 openms-thirdparty are external tools that are wrapped in OpenMS with adapters. This is required to use the adapters in
 the openms package.
 ```
 
 via `bioconda` for release versions
 
-````{tab} openms
-```bash
+```{code-tab} bash openms
 conda install openms
 ```
-````
 
-````{tab} libopenms
-```bash
+```{code-tab} bash libopenms
 conda install libopenms
 ```
-````
 
-````{tab} pyopenms
-```bash
+```{code-tab} bash pyopenms
 conda install pyopenms
 ```
-````
 
-````{tab} openms-thirdparty
-```bash
+```{code-tab} bash openms-thirdparty
 conda install openms-thirdparty
 ```
-````
 
 or our own `openms` channel for nightly snapshots (which are build based on the same bioconda dependencies)
 
-````{tab} openms
-```bash
+```{code-tab} bash openms
 conda install -c openms openms
 ```
-````
 
-````{tab} libopenms
-```bash
+```{code-tab} bash libopenms
 conda install -c openms libopenms
 ```
-````
 
-````{tab} pyopenms
-```bash
+```{code-tab} bash pyopenms
 conda install -c openms pyopenms
 ```
-````
 
-````{tab} openms-thirdparty
-```bash
+```{code-tab} bash openms-thirdparty
 conda install -c openms openms-thirdparty
 ```
-````
 
 ## Install via Debian package
 
@@ -155,24 +139,19 @@ project provide native containers from our bioconda packages for both Docker and
 
 Images of the containers can be pulled via or one of the following commands:
 
-````{tab} Docker
-```bash
+```{code-tab} bash Docker
 docker pull quay.io/biocontainers/libopenms
 docker pull quay.io/biocontainers/openms
 docker pull quay.io/biocontainers/pyopenms
 docker pull quay.io/biocontainers/openms-thirdparty
 ```
-````
 
-````{tab}Singularity
-```bash
+```{code-tab} bash Singularity
 docker pull https://depot.galaxyproject.org/singularity/libopenms
 docker pull https://depot.galaxyproject.org/singularity/openms
 docker pull https://depot.galaxyproject.org/singularity/pyopenms
 docker pull https://depot.galaxyproject.org/singularity/openms-thirdparty
 ```
-````
-
 If Singularity images fail to download or run, try to use the Docker images as Singularity will automatically convert them.
 
 Docker images from our own continuous integration can be installed via the following commands:

From 46cd6cc8b0bf9b4d0b01433e87e637dad4b1e4fa Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:24:14 +0530
Subject: [PATCH 13/14] Revert "Fix"

This reverts commit eaf3a63f1dae721a065f13ce33e39db874520209.
---
 docs/installations/installation-on-gnu-linux.md | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
index 4ba01965..ed540d21 100644
--- a/docs/installations/installation-on-gnu-linux.md
+++ b/docs/installations/installation-on-gnu-linux.md
@@ -8,12 +8,11 @@ obtain release versions (`bioconda` channel) and nightly versions (`openms` chan
 
 1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
 2. Add channels for dependencies:
-   ```bash
+   ```
     conda config --add channels defaults
     conda config --add channels bioconda
     conda config --add channels conda-forge
-   ```
-3. Install any of the following packages related to OpenMS
+4. Install any of the following packages related to OpenMS
 
 ```{group-tab} openms
 openms contains OpenMS C++ Tools.
@@ -156,7 +155,7 @@ If Singularity images fail to download or run, try to use the Docker images as S
 
 Docker images from our own continuous integration can be installed via the following commands:
 
-```bash
+```
 docker pull ghcr.io/openms/openms-library
 docker pull ghcr.io/openms/openms-executables
 ```

From 6113117d3f60780bb16e5f3da6b3110c740764af Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Mon, 13 Jun 2022 08:26:14 +0530
Subject: [PATCH 14/14] Revert "Major fix of installation instructions"

This reverts commit ab7106e25089d3c2b29d2b888901352aea820896.
---
 .../installation-on-gnu-linux.md              | 107 +++++-------------
 1 file changed, 30 insertions(+), 77 deletions(-)

diff --git a/docs/installations/installation-on-gnu-linux.md b/docs/installations/installation-on-gnu-linux.md
index ed540d21..a8d7c3ed 100644
--- a/docs/installations/installation-on-gnu-linux.md
+++ b/docs/installations/installation-on-gnu-linux.md
@@ -3,68 +3,41 @@ Installation on GNU/Linux
 
 ## Install via Conda
 
-You can use conda to install the OpenMS library and tools without user interface. Depending on the conda channel, you can
-obtain release versions (`bioconda` channel) and nightly versions (`openms` channel).
+Use conda or bioconda to install OpenMS.
 
 1. Follow the instructions to [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html).
-2. Add channels for dependencies:
+2. Install OpenMS using conda:
+   `conda install -c openms openms`
+3. Other OpenMS packages can be installed using:
+   ```
+   conda install -c openms pyopenms
+   conda install -c openms openms-thirdparty
+   conda install -c openms libopenms
    ```
-    conda config --add channels defaults
-    conda config --add channels bioconda
-    conda config --add channels conda-forge
-4. Install any of the following packages related to OpenMS
 
-```{group-tab} openms
+```{tab} openms
 openms contains OpenMS C++ Tools.
 ```
 
-```{group-tab} libopenms
+```{tab} libopenms
 libopenms is the C++ library required for the OpenMS C++ Tools to work.
 ```
 
-```{group-tab} pyopenms
+```{tab} pyopenms
 pyopenms is the python package that allows to use algorithms from libopenms in Python.
 ```
 
-```{group-tab} openms-thirdparty
+```{tab} openms-thirdparty
 openms-thirdparty are external tools that are wrapped in OpenMS with adapters. This is required to use the adapters in
 the openms package.
 ```
 
-via `bioconda` for release versions
-
-```{code-tab} bash openms
-conda install openms
-```
-
-```{code-tab} bash libopenms
-conda install libopenms
-```
-
-```{code-tab} bash pyopenms
-conda install pyopenms
-```
-
-```{code-tab} bash openms-thirdparty
-conda install openms-thirdparty
-```
+To install using bioconda:
 
-or our own `openms` channel for nightly snapshots (which are build based on the same bioconda dependencies)
-
-```{code-tab} bash openms
-conda install -c openms openms
 ```
-
-```{code-tab} bash libopenms
-conda install -c openms libopenms
-```
-
-```{code-tab} bash pyopenms
-conda install -c openms pyopenms
-```
-
-```{code-tab} bash openms-thirdparty
-conda install -c openms openms-thirdparty
+conda install -c bioconda openms
+conda install -c bioconda libopenms
+conda install -c bioconda openms-thirdparty
 ```
 
 ## Install via Debian package
@@ -118,54 +91,34 @@ Debian package.
 Some thirdparty software used via adapter tools in OpenMS might also require an installed JavaVM.
 ```
 
-## Run via a (Bio)Container
+## Run via a (Bio)Docker image
 
-Install a containerization software (e.g., [Docker](https://docs.docker.com/engine/install/) or [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps))
+Make sure you have [Docker installed](https://docs.docker.com/engine/install/).
 
-Our container support is constantly updated. Docker images provided by us,
-can be obtained via [ghcr.io](https://ghcr.io).
+Our Docker support is constantly updated. Images can be obtained via [ghcr.io](https://ghcr.io).
 
-1. [openms-executables](https://ghcr.io/openms/openms-executables)
-2. [openms-library](https://ghcr.io/openms/openms-library)
+1. [openms-executables](https://ghcr.io/openms/openms-executables:latest)
+2. [openms-library](https://ghcr.io/openms/openms-library:latest)
 
-Otherwise, the [BioContainers Registries](https://biocontainers.pro/registry) and the associated Galaxy
-project provide native containers from our bioconda packages for both Docker and Singularity.
+Or via [BioContainers Registeries](https://biocontainers.pro/registry).
 
 1. [BioContainers libopenms](https://biocontainers.pro/tools/libopenms)
 2. [BioContainers openms](https://biocontainers.pro/tools/openms)
 3. [BioContainers openms-thirdparty](https://biocontainers.pro/tools/openms-thirdparty)
 4. [BioContainers pyOpenMS](https://biocontainers.pro/tools/pyopenms)
 
-Images of the containers can be pulled via or one of the following commands:
+Docker images can be pulled via or one of the following commands:
 
-```{code-tab} bash Docker
-docker pull quay.io/biocontainers/libopenms
-docker pull quay.io/biocontainers/openms
-docker pull quay.io/biocontainers/pyopenms
-docker pull quay.io/biocontainers/openms-thirdparty
 ```
-
-```{code-tab} bash Singularity
-docker pull https://depot.galaxyproject.org/singularity/libopenms
-docker pull https://depot.galaxyproject.org/singularity/openms
-docker pull https://depot.galaxyproject.org/singularity/pyopenms
-docker pull https://depot.galaxyproject.org/singularity/openms-thirdparty
+docker pull biocontainers/openms
+docker pull openms/library
+docker pull openms/executables
+docker pull openms/pyopenms
 ```
-If Singularity images fail to download or run, try to use the Docker images as Singularity will automatically convert them.
-
-Docker images from our own continuous integration can be installed via the following commands:
-
-```
-docker pull ghcr.io/openms/openms-library
-docker pull ghcr.io/openms/openms-executables
-```
-
-per default this results in the download of the latest nightly snapshot. Specify a release version to
-receive a stable version.
-
-Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) yourself can be found on
-GitHub in our [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository.
 
 ## Build OpenMS from source
 
 To build OpenMS from source, follow the build instructions for [Linux](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/install_linux.html).
+
+Dockerfiles to build different kind of images (corresponding to build instructions, e.g. on ArchLinux) can be found on
+GitHub in [OpenMS/dockerfiles](https://github.com/OpenMS/dockerfiles) repository.