Merge pull request #25

Update installation instructions after #21

README.md

@@ -1,43 +1,67 @@
 
 # WARNING: The `main` branch is not production-ready
 
-The `main` branch is a prototype of newly refined architecture and it does not yet contain the functionalities we have reported previously. For a running version of HADDOCK3 please refer to the `alpha1` or the release page. However, we won't develop `alpha1` further. Stay tuned for new updates on the `main` branch as we are activily working on it. Cheers!
+The `main` branch is a prototype of newly refined architecture and it
+does not yet contain the functionalities we have reported previously.
+For a running version of HADDOCK3 please refer to the `alpha1` or the
+release page. However, we won't develop `alpha1` further. Stay tuned for
+new updates on the `main` branch as we are activily working on it.
+Cheers!
 
 * * *
 
 # HADDOCK3
 ## 1. Installation
 
-* Clone this repository:
+### 1.1 Clone this repository:
 
 ```bash
-git clone -b beta1 https://github.com/haddocking/haddock3.git
+git clone https://github.com/haddocking/haddock3.git
 cd haddock3
 ```
 
-* Create a virtual environment with Python 3.8+ and install dependencies:
+### 1.2 Create a virtual environment with Python 3.8+ and install dependencies:
+#### with `venv`
 
 ```bash
 virtualenv-3.8 venv
 source venv/bin/activate
 pip install -r requirements.txt
 ```
 
-* Activate and copy CNS binary to the expected path:
+#### with `conda`
+```bash
+conda env create -f requirements.yml
+conda activate haddock3
+```
+
+### 1.3 Copy CNS binary to the expected path:
 
 ```bash
-source bin/activate_haddock
 mkdir -p bin/cns
-cp /path/to/cns_solve-1.31-UU-MacIntel.exe bin/cns
+
+# on mac
+ls -s bin/cns /PATH/TO/cns_solve-1.31-UU-MacIntel.exe
+
+# on linux
+ls -s bin/cns /PATH/TO/CNS_FOLDER/intel-x86_64bit-linux/source/cns_solve-2002171359.exe
 ```
 
-* Define some addiational environmental variables:
+### 1.4 Activate environment variables
+
+Edit the file `bin/activate_haddock` and change the value in
+`HADDOCK3_NUM_CORES` variable to the number of CPU cores you wish
+`haddock3` to use. For example, to use 4 cores:
 
 ```bash
-export HADDOCK3_NUM_CORES=8
-export HADDOCK3_CNS_EXE="/path/to/haddock3/bin/cns/cns_solve-1.31-UU-MacIntel.exe"
+export HADDOCK3_NUM_CORES=4
 ```
 
+Save and exit. Source the file:
+
+```bash
+source bin/activate_haddock
+```
 
 ## 2. Examples
 
@@ -47,4 +71,3 @@ export HADDOCK3_CNS_EXE="/path/to/haddock3/bin/cns/cns_solve-1.31-UU-MacIntel.ex
 cd examples/recipes/scoring/
 haddock3.py scoring.toml
 ```
-

bin/activate_haddock

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+export HADDOCK3_NUM_CORES=4
 export HADDOCKPATH=`pwd`
 export PYTHONPATH=$PYTHONPATH:$HADDOCKPATH
 export PATH=$PATH:$HADDOCKPATH/bin
+export HADDOCK3_CNS_EXE="${HADDOCKPATH}/bin/cns"

requirements.yml

@@ -0,0 +1,13 @@
+name: haddock3
+channels:
+    - conda-forge
+    - defaults
+dependencies:
+    - python==3.8
+    - pip
+    - numpy
+    - toml
+    - jsonpickle
+    - pip:
+        - pdb-tools
+        - lightdock