2. Getting started

2.1. Introduction

This first chapter is a brief guide to setting-up the STK on Linux, Windows and MacOS X. STK comes as either pre-compiled binaries for some platform or as a source package. Both downloading an archived source package or downloading via bzr are covered. We assume little knowledge of Linux or DOS commands, but some knowledge on how to install software. Contact your local sys admin if you need further help.

We store all source code and downloads on Canonical’s Launchpad system: http://launchpad.net/supertree-toolkit

2.2. Linux

The STK is distributed via Launchpad PPA. You need to add the Supertree Toolkit PPA (https://launchpad.net/~stk-developers/+archive/release) to your system, along with an additional one which contains some dependencies. You can then install the package. Run the commands below to do all this.

sudo apt-add-repository ppa:fluidity-core/ppa
sudo apt-add-repository ppa:stk-developers/release
sudo apt-get update
sudo apt-get -y install supertree-toolkit

This will install the GUI and CLI to standard locations and add the GUI to your Applications menu.

2.3. Windows

A pre-built binary package is available. Simply download and run to install. Follow the on-screen instructions.

The STK CLI is also available from a Command Prompt.

2.4. MacOS X

A DMG is available on Launchpad. Drag the STK icon into the Applications folder. This will install the STK GUI on your Mac.

To install the CLI you must alter your PATH and PYTHONPATH variables. To do this permanently, edit your .bash_profile file and add the following lines:

export PYTHONPATH=$PYTHONPATH:\
/Applications/STK.app/Contents/Resources/lib/python2.7/site-packages/
export PATH=/Applications/STK.app/Contents/Resources/bin/:$PATH

You can access the STK CLI from a standard terminal

2.5. Source

The source is available as either a compressed tarball or via bzr. To obtain the tarball, simply download from Launchpad, then:

tar zxvf supertree-toolkit.tgz

Using bzr, you can either obtain the bleeding-edge development version or the current release (recommended) using:

bzr branch lp:supertree-toolkit/trunk

or

bzr branch lp:supertree-toolkit/release

respectively.

Regardless of how the source was obtained, you can now either use the STK in-place or install it using:

sudo python setup.py install

(for Windows users, the sudo is not required).

2.5.1. Prerequisites and dependencies

When running from source you must install the following prerequisites and dependencies:

2.6. Running the STK

There are two ways to run the STK: via the GUI (Graphical User Interface) or the CLI (Command Line Interface). Most data collecting and curation is done via the GUI. However, either can be used to carry out data processing. The CLI also contains a few more utility functions that are not available in the GUI.

The GUI is run from the command line using:

stk-gui

The CLI version is run using:

stk

which will produce the following help.

usage: stk [-h] [-v] [-i]

        {create_matrix,sub_taxa,import_data,export_data,export_trees,export_bib,
         data_summary,safe_taxonomic_reduction,data_ind,data_overlap,permute_trees,
         clean_data,replace_genera,convert_files,create_subset}
        ...
stk: error: too few arguments

The STK GUI can also be accessed via the Start Menu (Windows), the Applications folder (Mac OS X) or in the Applications menu (most Linux variants).