setup.rst

Setup

Prerequisites

• Python

For this tutorial it is recommended to use the anaconda python distribution. Download anaconda (Python 3.6 version) from https://www.continuum.io/downloads for Linux x86_64 and follow the installation instructions on the download page. Make sure that python from this installation is in your $PATH. In addition the following python packages must be installed:

pip install --upgrade pip
pip install pjson
pip install pyaml
pip install future
pip install python-igraph

• MongoDB

If your system is Ubuntu and you have administrator permissions you can install MongoDB system-wide with the following command:

sudo apt-get install mongodb

The server is automatically started after the installation is completed.

For general instructions please read the installation manual https://docs.mongodb.com/manual/administration/install-on-linux/

Install FireWorks

The following instructions are for installation in your $HOME directory. You might like to create another directory for this tutorial and replace $HOME with the relevant path.

cd $HOME
git clone https://github.com/ikondov/fireworks
cd fireworks
python setup.py develop --user
export PYTHONPATH=$PWD:$PYTHONPATH
export PATH=$HOME/.local/bin:$PATH

Install the tutorial

cd $HOME
git clone https://git.scc.kit.edu/jk7683/gridka-school-fireworks
cd gridka-school-fireworks
export PYTHONPATH=$PWD/lib:$PYTHONPATH
export PATH=$PWD/bin:$PATH

Further packages

In order to visualize the workflows graphically two packages must be installed:

sudo apt-get install graphviz evince

The packages ImageMagick and Eye of GNOME (eog) are necessary for Exercise 3:

sudo apt-get install imagemagick eog

If editors like vi or nano are not preferred, more advanced editors may be installed, e.g.:

sudo apt-get install gedit emacs

For the web GUI of lpad a web browser must be installed, e.g.:

sudo apt-get install firefox