HYDROID

HYDROID: Installation instructions

Quick installation options

Using Anaconda Python distribution (Mac, Linux, Windows(only HYDROIDexp module))

Install Miniconda with Python2.7 for your platform from https://conda.io/miniconda.html. Open terminal (Anaconda terminal on Windows) and run:

conda install -c hydroid hydroid

Test HYDROID:

HYDROID_test_exp #Tests exeprimental data analysis module
HYDROID_test_pred #Tests molecular structure analysis module

Using PyPI and pip with native Python

Have Python2.7 and pip installed. Open terminal and run:

pip install hydroid

To enable functionality of HYDROIDpred module (currently for Mac and Linux) compile and install freesasa library v2.0.2.

Test HYDROID:

HYDROID_test_exp #Tests exeprimental data analysis module
HYDROID_test_pred #Tests molecular structure analysis module

Generic instructions for advanced users

Requirements

Python 2.7
Python modules specified in requirements.txt. May be installed with pip install -r requirements.txt
freesasa library v2.0.2 should be compiled with python bindings and accessible in python (only needed for HYDROIDpred module).
Manual installation

After installing the required components, download and unarchive the latest release of HYDROID. Run:
```
python setup.py install
```

From scratch copy-paste instructions on various platforms (using virtual environments)

Below we provide several copy-paste examples for different operating systems using native Python and separating the install into a virtual environment.

On Ubuntu Linux (v16.04 x64) with native Python

Open bash terminal an execute following commands.

#prepare package manager and core packages
sudo apt-get install software-properties-common
sudo apt-add-repository universe
sudo apt-get update
sudo apt-get -y install python-pip
sudo apt-get -y install python-tk

#Enable virtualenv
pip install virtualenv
virtualenv venv
source venv/bin/activate
pip install --upgrade pip

#Install HYDROID
pip install https://github.com/ncbi/HYDROID/archive/master.tar.gz

#Install FREESASA (optional, only for HYDROIDpred)
pip install Cython
wget https://github.com/mittinatten/freesasa/releases/download/2.0.2/freesasa-2.0.2.tar.gz
mkdir freesasa
tar -zxf freesasa-2.0.2.tar.gz -C freesasa --strip-components=1
cd freesasa
./configure --enable-python-bindings --disable-json --disable-xml CFLAGS="-fPIC -O2" --prefix=`pwd`
make; make install

#Test that it's working
HYDROID_test_exp #Tests exeprimental data analysis module
HYDROID_test_pred #Tests molecular structure analysis module

On MacOS with native Python:

Open Terminal an execute following commands.

#Enable virtualenv
pip install virtualenv
virtualenv venv
source venv/bin/activate
pip install --upgrade pip
pip install wget

#Install HYDROID
pip install https://github.com/ncbi/HYDROID/archive/master.tar.gz

#Install FREESASA (optional, only for HYDROIDpred)
pip install Cython
python -m wget https://github.com/mittinatten/freesasa/releases/download/2.0.2/freesasa-2.0.2.tar.gz
mkdir freesasa
tar -zxf freesasa-2.0.2.tar.gz -C freesasa --strip-components=1
cd freesasa
./configure --enable-python-bindings --disable-json --disable-xml CFLAGS="-fPIC -O2" --prefix=`pwd`
make; make install
cd ..

#MacOS specific stuff
deactivate
export PYTHONHOME=`pwd`/venv

#Test that it's working
python
from hydroid.command_line import test_exp, test_pred
test_exp()
test_pred()

On MacOS with Continuum Anaconda Python

First, install Miniconda with Python2.7 from https://conda.io/miniconda.html.

Then open terminal an execute following commands.

conda install wget

#download HYDROID
wget --no-check-certificate https://github.com/ncbi/HYDROID/archive/master.tar.gz
tar -zxf master.tar.gz
cd HYDROID-master

#Create environments and install packages
conda env create -f conda_env.yml
source activate hydroid

#Install HYDROID
python setup.py install

#Install FREESASA (optional, only for HYDROIDpred)
conda install Cython
wget --no-check-certificate https://github.com/mittinatten/freesasa/releases/download/2.0.2/freesasa-2.0.2.tar.gz
mkdir freesasa
tar -zxf freesasa-2.0.2.tar.gz -C freesasa --strip-components=1
cd freesasa
./configure --enable-python-bindings --disable-json --disable-xml CFLAGS="-fPIC -O2" --prefix=`pwd`
make; make install
cd ..

#Test that it's working
HYDROID_test_exp #Tests exeprimental data analysis module
HYDROID_test_pred #Tests molecular structure analysis module

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