update docs (#156)

Author: rvhonorato

README.md

@@ -89,12 +89,13 @@ Use the pre-compiled binaries from the latest release
 **Check the step-by-step tutorial at [bonvinlab.org/education/haddock-runner](https://www.bonvinlab.org/education/haddock-runner/)**
 
 ```bash
-Usage: haddockrunner [options] <input file>
+Usage: haddock-runner [options] <input file>
 
-Run HADDOCK benchmarking
+Run HADDOCK on a dataset of complexes
 
 Options:
   -version: Print version and exit
+  -setup: Only perform the setup, do not execute the benchmark
 ```
 
 - `input.yml`

docs/src/home.md

@@ -2,13 +2,16 @@
 
 ![image](./banner_home-mini.jpg)
 
-The `haddock-runner` is an effort to reduce code duplication and to streamline the execution of HADDOCK benchmarks.
+The `haddock-runner` is an effort to reduce code duplication and to streamline
+the execution of HADDOCK benchmarks.
 
 It is a standalone program, freely available at [https://github.com/haddocking/haddock-runner](https://github.com/haddocking/haddock-runner).
 
-It is designed to be used with both the production-ready [HADDOCK2.4](/software/haddock2.4), the pre-release _HADDOCK2.5_ and the experimental (unpublished) [HADDOCK3](/software/haddock3) versions.
+It is designed to be used with both [HADDOCK2.4/5](/software/haddock2.4), and
+[HADDOCK3](/software/haddock3) versions.
 
-When running a benchmark, users/developers may be interested in the following (in no specific order):
+When running a benchmark, users/developers may be interested in the following
+(in no specific order):
 
 - The quality of the docking results when using different parameters
 - Comparing the results of different versions
@@ -18,4 +21,5 @@ Have a look at the menu on the left for more information on how to use it.
 
 ## Getting help
 
-If you encounter any issues or have any questions, please open an issue on the [GitHub repository](https://github.com/haddocking/haddock-runner), contact us at _[email protected]_ or join the [BioExcel forum](https://ask.bioexcel.eu) and post your question there.
+If you encounter any issues or have any questions, please open an issue on the
+[GitHub repository](https://github.com/haddocking/haddock-runner), contact us at _[email protected]_ or join the [BioExcel forum](https://ask.bioexcel.eu) and post your question there.

docs/src/how-does-it-work.md

@@ -3,7 +3,6 @@
 The execution of the `haddock-runner` consists of a few steps:
 
 1. Set up the benchmark
-
    - Copy the target structures to the location where the HADDOCK run will be executed
 
 2. Set up the HADDOCK run

docs/src/installation.md

@@ -1,32 +1,42 @@
 # Installation
 
-The tool is designed for users/students/developers that are familiar with HADDOCK and command-line scripting, and have access to an HPC infrastructure.
+The tool is designed for users/students/developers that are familiar with
+HADDOCK and command-line scripting, and have access to an HPC infrastructure.
 
-If this is the first time you are using HADDOCK, please first familiarize yourself with the software by running the basic [HADDOCK2.4](/education/HADDOCK24/index.md) or [HADDOCK3](/education/HADDOCK3/index.md) tutorials.
+If this is the first time you are using HADDOCK, please first familiarize
+yourself with the software by running the basic
+[HADDOCK2.4](/education/HADDOCK24/index.md) or [HADDOCK3](/education/HADDOCK3/index.md) tutorials.
 
-This tool is not meant to be used by end-users who want to run a single target, or a small set of targets; for that purpose we recommend instead using the [HADDOCK2.4 web server](https://wenmr.science.uu.nl/haddock2.4/).
+This tool is not meant to be used by end-users who want to run a single target,
+or a small set of targets; for that purpose we recommend instead using
+the [HADDOCK2.4 web server](https://wenmr.science.uu.nl/haddock2.4/).
 
 > **VERY IMPORTANT**: You need to have HADDOCK installed on your system.
 > This is not covered in this documentation.
-> Please refer to the [HADDOCK2.4 installation instructions](/software/haddock2.4/installation) or [HADDOCK3.0 repository](https://github.com/haddocking/haddock3) for more information.
+> Please refer to the
+> [HADDOCK2.4 installation instructions](/software/haddock2.4/installation)
+> or [HADDOCK3.0 repository](https://github.com/haddocking/haddock3) for more information.
 
-`haddock-runner` is a standalone open-source software licensed under Apache 2.0 and freely available from the following repository: [github.com/haddocking/haddock-runner](https://github.com/haddocking/haddock-runner).
+`haddock-runner` is a standalone open-source software licensed under Apache 2.0
+and freely available from the following repository: [github.com/haddocking/haddock-runner](https://github.com/haddocking/haddock-runner).
 
 To use it simply download the latest binary from the [releases page](https://github.com/haddocking/haddock-runner/releases):
 
 ```bash
-$ wget https://github.com/haddocking/haddock-runner/releases/download/v1.10.0/haddock-runner_1.10.0_linux_386.tar.gz
-$ tar -zxvf haddock-runner_1.10.0_linux_386.tar.gz
+$ wget https://github.com/haddocking/haddock-runner/releases/download/v1.13.0/haddock-runner_1.13.0_linux_386.tar.gz
+$ tar -zxvf haddock-runner_1.13.0_linux_386.tar.gz
 $ ./haddock-runner -version
-haddock-runner version v1.10.0
+haddock-runner version v1.13.0
 ```
 
-Alternatively, you can build the latest version from source (you probably don't need to do that), make sure [go](https://go.dev/doc/install) is installed and run the following commands:
+Alternatively, you can build the latest version from source (you probably don't
+need to do that), make sure [go](https://go.dev/doc/install) is installed
+and run the following commands:
 
 ```bash
 $ git clone https://github.com/haddocking/haddock-runner.git
 $ cd haddock-runner
 $ go build -o haddock-runner
 $ ./haddock-runner -version
-haddock-runner version v1.10.0
+haddock-runner version v1.13.0
 ```

docs/src/usage.md

@@ -4,5 +4,5 @@ This chapter will go over the steps needed to use `haddock-runner`.
 
 1. [Writing the input file list of the targets `input.list`](./writing-a-input.list-file.md)
 2. [Writing a `run-haddock.sh` script](./writing-a-run-haddock.sh-script.md)
-3. [Preparing the configuration file, `benchmark.yaml`](./writing-the-benchmark.yaml-file.md)
+3. [Preparing the configuration file, `benchmark.yaml`](./writing-a-benchmark.yaml-file.md)
 4. [Running `haddock-runner`](./running-haddock-runner.md)