Installation

Binaries and Installers

Note

The installers only provide the GUI version of TriFusion. If you want to install both the GUI and command line versions, check the Installation from source.

The easiest way to install TriFusion is through binaries and installers provided for Windows, MacOS and Linux.

Linux

Installation from source

TriFusion is available on PyPi nd can be easily installed with pip . This will only install the command line versions of TriFusion (TriSeq, TriStats and orthomcl_pipeline). Therefore, if you are interested only in the command line version of TriFusion, and assuming you have python2.7 and pip on your system, installing TriFusion is simply:

pip install trifusion

The dependencies for the graphical user interface require only a few extra commands that are provided below for each operating system.

Windows

Windows does not come with a python installation by default. We recommend using a package manager, such as Anaconda, which automatically installs most of the dependencies (Note that TriFusion requires python2.7). After installing python, you will need to install kivy by executing the following commands on a command line prompt:

python -m pip install --upgrade pip wheel setuptools
python -m pip install docutils pygments pypiwin32 kivy.deps.sdl2 kivy.deps.glew
python -m pip install kivy.deps.gstreamer --extra-index-url https://kivy.org/downloads/packages/simple/
python -m pip install kivy

Then, install trifusion by typing:

pip install trifusion

MacOS (using homebrew)

f you do not have homebrew yet, you’ll need to install it:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Then, to install TriFusion and it’s dependencies:

brew install sdl2 sdl2_image sdl2_ttf sdl2_mixer
pip install -I Cython==0.23
USE_OSX_FRAMEWORKS=0 pip install kivy
pip install trifusion

Ubuntu (and relatives)

On Ubuntu, there are PPAs available for the installation of TriFusion via apt-get in addition to the pip installation method.

Via PPA

  • Add one of the following PPAs:
    # Stable release:
sudo add-apt-repository ppa:o-diogosilva/trifusion
# Daily release:
sudo add-apt-repository ppa:o-diogosilva/trifusion-daily
  • Upgrade your package list and install TriFusion:
    sudo apt-get update && sudo apt-get install trifusion

Via pip

sudo apt-get install python-pip build-essential python-dev libsdl2-dev
pip install cython==0.23
pip install kivy
pip install trifusion

Debian

As with Ubuntu, you may install TriFusion via the available PPAs or with pip.

Via PPA

  • Add one of the following PPAs manually to the sources.list file:
    # Stable release:
http://ppa.launchpad.net/o-diogosilva/trifusion/ubuntu trusty main
# Daily release:
http://ppa.launchpad.net/o-diogosilva/trifusion-daily/ubuntu trusty main
  • Add the GPG key to your apt keyring:
    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys D4F1E8E6
  • Upgrade your package list and install TriFusion:
    sudo apt-get update && sudo apt-get install trifusion

Via pip

sudo apt-get install python-pip build-essential python-dev libsdl2-dev
pip install cython==0.23
pip install kivy
pip install trifusion

RPM based

dnf install python-pip python-devel redhat-rpm-config freeglut-devel SDL* libsdl2-dev
pip install cython==0.23
pip install kivy
pip install trifusion

ArchLinux

There are three AUR packages for TriFusion:

  • trifusion: The latest release of TriFusion, based on source code.
  • trifusion-bin: The latest release of TriFusion. in binary format. Does not require dependencies to be installed, as all the necessary libs are bundled with the distributed binary
  • trifusion-git: The bleeding edge version directly from git. Requires dependencies to be installed, as it is also source code based.

Just use any AUR helper to handle the packages for you, or download the PKGBUILD you require and use makepkg.