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Update README.md #1146

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42 changes: 26 additions & 16 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,30 +23,21 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**

## Installation

Simple installation of the [latest release](https://pypi.org/project/haddock3/) of HADDOCK3.

```bash
pip install haddock3
```

Execute:
In case you rather install the latest unreleased version use instead:

```bash
$ haddock3 -h
usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe

positional arguments:
recipe The input recipe file path

optional arguments:
-h, --help show this help message and exit
--restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
--extend-run EXTEND_RUN
Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
--setup Only setup the run, do not execute
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
-v, --version show version
git clone https://github.com/haddocking/haddock3.git
cd haddock3
pip install .
```

For the installation of third-party additional software, please check the [INSTALL](docs/INSTALL.md).
For detailed instructions and installation of third-party software, please check [INSTALL.md](docs/INSTALL.md)

You might also want to check the following utilities:

Expand All @@ -62,6 +53,25 @@ The most basic usage is:
haddock3 <configuration-file.toml>
```

For help on haddock3 usage:

```bash
$ haddock3 -h
usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe

positional arguments:
recipe The input recipe file path

optional arguments:
-h, --help show this help message and exit
--restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
--extend-run EXTEND_RUN
Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
--setup Only setup the run, do not execute
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
-v, --version show version
```

Check the [EXAMPLES](https://github.com/haddocking/haddock3/blob/main/examples/README.md) page for more some usage examples and the [MANUAL]() (_coming soon!_) for a more detailed explanation of the configuration file.

## Support
Expand Down