1. Krister Swenson Avatar Krister Swenson
  2. Phage Recombination
  3. Alpha

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Alpha / Installation Instructions

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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

  1. Download the installer script: wget https://bitbucket.org/thekswenson/alpha/raw/master/installscript/installalpha
  2. Make it executable: chmod +x installalpha
  3. Run it: ./installalpha
  4. 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 then alpha/bin/alpha -h

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:

  1. 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

  2. Do the support package installation steps for Conda or Homebrew as described below.

  3. Build and install

    • cd ~/alphadir/alpha
    • ./setup.py build
    • python3 -m pip install .

With Conda (less invasive)

  1. Install Miniconda
  2. Create a conda environment conda create --name alphaenv
  3. Activate environment conda activate alphaenv

  4. Install conda packages

    • conda install graphviz pkg-config
    • conda install -c conda-forge gtk3 pygobject librsvg adwaita-icon-theme fonts-conda-forge glib

  5. 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

  6. 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)

  7. 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.

  1. Install Homebrew (cut and paste the command at that page)

  2. 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

  3. 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)

  4. 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)
  5. Go back and finish the instructions from the top of this section

Windows

  1. Follow the simple windows install instructions on the main page.
  2. Follow the Ubuntu Linux instructions above.

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