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Update installation instructions #1039

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update installation instructions
rvhonorato Sep 20, 2024
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Update README.md
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29 changes: 28 additions & 1 deletion README.md
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Expand Up @@ -26,7 +26,34 @@ HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**

## Installation

Please check the [INSTALL](docs/INSTALL.md) file for instructions.
Clone the repository and run `pip install`;

```bash
git clone https://github.com/haddocking/haddock3
cd haddock3
pip install .
```

Execute:

```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 onward will be deleted.
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--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
```

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

You might also want to check the following utilities:

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123 changes: 13 additions & 110 deletions docs/INSTALL.md
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@@ -1,130 +1,31 @@
# Installation

Open a `terminal` window and navigate to the folder where you want to
install HADDOCK3; for example: `software`. The current installation
instructions are local and will affect only your user.

Before starting with the installation of HADDOCK3, make sure to properly [install CNS](CNS.md).
If you have installed a previous version of HADDOCK, you may already have a suitable version of CNS.
Please do [check your CNS installation](CNS.md#5-Check-installation) before proceeding.


## 1. Clone this repository:

Mind the `--recursive` flag when cloning!

```bash
git clone --recursive https://github.com/haddocking/haddock3.git
```

Go to the **haddock3** directory

```bash
cd haddock3
```

and type the following commands to first install the [FCC](https://github.com/haddocking/fcc) source code provided

```bash
cd src/fcc/src
chmod u+x Makefile
make
cd -
```

Then, follow the same logic to install the [fast-rmsdmatrix](https://github.com/mgiulini/fast-rmsdmatrix) source code

```bash
cd src/fast-rmsdmatrix/src
chmod u+x Makefile
make fast-rmsdmatrix
cd -
```

By the end of the above commands, you should be back to the **haddock3**
main folder.

## 2 Create a virtual environment with Python 3.9+ and install dependencies:
Create a virtual environment with Python 3.10:

You can use Python's `venv` or `conda` depending on your choice.
Commands are provided below:

### with `venv`

```bash
virtualenv venv --python=3.9
virtualenv venv --python=3.10
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Why python3.10? We have always been using 3.9 (which is still quite distributed on various OS). Will it work with both 3.9 and 3.10? Has haddock3 been tested on 3.10?

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Yes

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Will address this in #1040

source venv/bin/activate
pip install -r requirements.txt
```

### with `conda`

```bash
conda create -n haddock3 python=3.9
conda create -n haddock3 python=3.10
conda activate haddock3
pip install -r requirements.txt
```

## 3. Install the HADDOCK3 package and command line clients

```bash
python setup.py develop --no-deps
```

Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS.

## 4. Make a CNS binary shortcut to the expected path:

```bash
mkdir -p bin/

# on mac
ln -s /PATH/TO/cns_solve_1.3/mac-intel-darwin/source/cns_solve-2206031450.exe bin/cns

# on linux
ln -s /PATH/TO/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2002171359.exe bin/cns
```

As long as you have the `(haddock3)` python environment activated, you can
navigate away from the **haddock3** installation folder. You can run
HADDOCK3 from anywhere. To run HADDOCK3, follow the [usage
guidelines](USAGE.md).


## 5. Keep your installation up to date

Navigate to the **haddock3** installation folder (the one you cloned from
GitHub). Ensure you have the `(haddock3)` python environment activated.
Please keep in mind that HADDOCK3, as well as its
dependencies, are under active development.
If the updating processing fails, it is safest to reinstall
from scratch. Always refer to the latest installation guidelines.

```bash
# if you used `venv`
source venv/bin/activate

# if you used `conda`
conda activate haddock3
```

Afterwards:

```bash
# pull the latest source code from our repository to your computer
git pull

# update the dependencies by running:
pip install -r requirements.txt --upgrade

# ensure all command-lines clients are installed
python setup.py develop --no-deps
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Do we have devel installation instructions somewhere else?

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I'm waiting for you to add the " developing haddock3 in HPC " at #988 :)

git clone https://github.com/haddocking/haddock3.git
cd haddock3
pip install .
```

Of note, here we are still using the depreacted `setup.py` command due to HPC, GRID and LOCAL compabilities with CNS.


## 6. (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI
## (Optional) Install MPI libraries if you intend to run HADDOCK3 with MPI

To use the mpi implementation of haddock3 you must have mpi4py installed in the `(haddock3)` python environment, and OpenMPI in the host system.

Expand All @@ -136,7 +37,7 @@ $ conda install -c conda-forge mpi4py

Later, you can find [here](https://www.bonvinlab.org/haddock3/tutorials/mpi.html) instructions on how to run HADDOCK3 with MPI.

## 7. (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service
## (Optional) Install web service dependencies if you intend to run HADDOCK3 restraints web service

To run the restraints web service you must have the following dependencies installed in the `(haddock3)` python environment:

Expand All @@ -146,21 +47,21 @@ pip install uvicorn fastapi

Information on the restraints web service can be found [here](https://github.com/haddocking/haddock3/blob/main/src/haddock/clis/restraints/webservice.py).

# Installing third-party packages
## Installing third-party packages

HADDOCK3 can integrate third-party software in its workflows.
We are not responsible for the proper installation of such packages, but
we help you install them. Below, you will find a list of all third-party
packages HADDOCK3 can use and guidelines for their proper installation.

## `lightdock`
### `lightdock` (outdated)

To install [lightdock](https://github.com/lightdock/lightdock) follow
the instructions on the project's website. Remember to install it under
the same Python environment you created for HADDOCK3. If you have any
doubts, please let us know.

## `gdock`
### `gdock` (outdated)

1. Clone the latest version:

Expand All @@ -170,11 +71,13 @@ git clone https://github.com/rvhonorato/gdock.git
```

2. Install Python3+ dependencies

```
pip install deap scipy mgzip biopython
```

3. Set `GDOCK_PATH`

```
export GDOCK_PATH=some-folder
```
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