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Alpha Installation
Simple Installation
See the main page for simple installation instruction for the most recent versions of Ubuntu, macOS, and Windows.
Manual Installation
You should try to use of of the packages we provide. If you want to modify something, or run Alpha on an older OS, you can follow these instructions.
Ubuntu Linux
- Download the installer script:
wget https://bitbucket.org/thekswenson/alpha/raw/master/installscript/installalpha
- Make it executable:
chmod +x installalpha
- Run it:
./installalpha
- Either install or run from this directory:
- Install to the system:
cd alpha; sudo python3 -m pip install .
- Run from here:
export PYTHONPATH=/PATH/TO/THE/DIR/alpha/src:$PYTHONPATH
and thenalpha/bin/alpha -h
- Install to the system:
MacOS
There are two options for macOS. The Conda version is less invasive than the Homebrew version. Both options share the first and last steps:
-
Clone the repositories
mkdir alphadir
cd alphadir
git clone --depth 1 https://thekswenson@bitbucket.org/thekswenson/alpha.git
git clone --depth 1 https://thekswenson@bitbucket.org/thekswenson/pyinclude.git
-
Do the support package installation steps for Conda or Homebrew as described below.
-
Build and install
cd ~/alphadir/alpha
./setup.py build
python3 -m pip install .
With Conda (less invasive)
- Install Miniconda
- Create a conda environment
conda create --name alphaenv
- Activate environment
conda activate alphaenv
-
Install conda packages
conda install graphviz pkg-config
conda install -c conda-forge gtk3 pygobject librsvg adwaita-icon-theme fonts-conda-forge glib
-
Install pip packages
python3 -m pip install --install-option="--include-path=$CONDA_PREFIX/include" --install-option="--library-path=$CONDA_PREFIX/lib" pygraphviz
python3 -m pip install numpy biopython networkx python-igraph matplotlib cython
-
export PYTHONPATH=~/alphadir/alpha/src/:$CONDA_PREFIX/lib/python3.8/site-packages/
(you'll have to do this each time you open a new terminal, or put it in your .bashrc) - Go back and finish the instructions from the top of this section
With Homebrew (more invasive)
We support the 3 most recent releases of macOS. Installation could be possible on older versions, but the main difficulty is due to the same policy used by Homebrew.
- Install Homebrew (cut and paste the command at that page)
-
Install brew packages
brew install glib gobject-introspection pygobject3 py3cairo libffi adwaita-icon-theme graphviz gtk+3
brew tap brew tap homebrew/cask-fonts
brew cask install font-liberation
-
Install pip packages with
python3 -m pip install cython networkx python-igraph numpy pygraphviz matplotlib biopython pygobject
(you could use a virtual environment if you choose) export PYTHONPATH=~/alphadir/alpha/src/:/usr/local/lib/python3.8/site-packages/
(you'll have to do this each time you open a new terminal, or put it in your .bashrc)- Go back and finish the instructions from the top of this section
Windows
- Follow the simple windows install instructions on the main page.
- Follow the Ubuntu Linux instructions above.
Updated