Installation

To install wft4galaxy as native Python library, you have to:

  1. clone the corresponding github repository:
git clone https://github.com/phnmnl/wft4galaxy
  1. install the package from source code using the usual Python setup.py:
python setup.py install [--user]

Note

Use the option --user to install the module only for the current user.

Warning

If are using a linux base system (like Ubuntu), probably you need to install the python-lxml and libyaml-dev packages as a further requirement.

Note

If want to use wft4galaxy with Docker, you can skip the two steps above: see Dockerized wft4galaxy for more details.

As a final step, you need to get an API KEY from your Galaxy instance, which can be done from the ‘User’ menu of the web Galaxy interface. This API KEY, together with the URL of your Galaxy instance (i.e., http://192.168.64.2:30700), must be provided to wft4galaxy in order for it to connect to and communicate with that server. This can be done either passing them as parameters to the command line script (see CLI options notebooks/1_run_suite_from_cli.ipynb) and to the the main API endpoints (see Programmatic Usage) or setting them as environment variables; i.e.:

export GALAXY_URL="<YOUR_GALAXY_SERVER_URL>"
export GALAXY_API_KEY="<YOUR_GALAXY_API_KEY>"

Docker-based Installation

wft4galaxy can also run within a Docker container, without installation.

To simplify the usage of the Docker images by command line, we provide a simple script mainly intended to allow users to interact with the dockerized version of the tool as if it was “native”, i.e., like a locally installed wft4galaxy. This script is called wft4galaxy-docker.

Installation

To install wft4galaxy-docker so that it is available system-wide, you can use the following command which will download and install the script to /usr/local/bin:

curl -s https://raw.githubusercontent.com/phnmnl/wft4galaxy/master/utils/docker/install.sh | bash

If your PATH includes /usr/local/bin you will have the wft4galaxy-docker script immediately available from your terminal. Alternatively, you can install the wft4galaxy-docker script in any other folder of your system by simply appending the string /dev/stdin <TARGET_FOLDER> to the line above, replacing TARGET_FOLDER with the folder you want to use for installation. For example, if you want to install the script to your current directory, cut and paste the following line to your terminal:

curl -s https://raw.githubusercontent.com/phnmnl/wft4galaxy/master/utils/docker/install.sh | bash /dev/stdin .

Then, type ./wft4galaxy-docker to launch from your current path.