GKSfromWorflows

GKSfromWorflows uses the python script galaxykickstart_from_workflow.py to quickly generate a GalaxyKickStart use case from one or several workflow files (.ga, note that these files must have been generated with galaxy >= release_16.04)

From GalaxyKickStart/scripts, run

python galaxykickstart_from_workflow.py --help

Then

python galaxykickstart_from_workflow.py -w <workflow1.ga> <workflow2.ga> ... -l <Panel_label>

This creates:

  • An inventory file GKSfromWorkflow in the inventory_filesfolder
  • A group_vars file GKSfromWorkflow in the group_varsfolder
  • A folder GKSfromWorkflowin the folder extra-files which will contain a copy of the workflow1.ga, workflow2.ga, ... files, plus a GKSfromWorkflow_tool_list.yml file that contains a yml description of all tools used in the workflows.

Note that running galaxykickstart_from_workflow.py overwrites these folders and files if they exist from a previous script run.

Adapt the created inventory file

Before running ansible-playbook, you have just to adapt the GKSfromWorkflow inventory_file inventory_files/GKSfromWorkflow to your own network settings (the file is preconfigured for running locally ansible-playbook on your target machine).

As usual, you may also tune the group_vars/all file.

Run the playbook

cd GalaxyKickStart
ansible-galaxy install -r requirements_roles.yml -p roles
ansible-playbook -i inventory_files/GKSfromWorkflow galaxy.yml

Check your running Galaxy instance after completion of the playbook. It contains the preinstalled tools as well as the workflow1, workflow2, etc....