Creating a tool_list.yml file
To install tools, you will need to prepare a list of tools in yaml format. A an example of a a tool list can be found in here
tools: - name: blast_to_scaffold owner: drosofff revisions: tool_panel_section_label: Metavisitor tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: blastx_to_scaffold owner: drosofff revisions: tool_panel_section_label: Metavisitor tool_shed_url: https://toolshed.g2.bx.psu.edu/ - name: bowtie2 owner: devteam revisions: - 019c2a81547a tool_panel_section_label: Metavisitor tool_shed_url: https://toolshed.g2.bx.psu.edu/
when the revision is empty, the latest available revision will be installed.
tool_panel_section_label will determine the tool panel section where the tools will be found.
Obtaining a tool_list.yml file
We can also obtain a tool list from a runnning galaxy instance. Note that for server running a galaxy release <16.04, you need a galaxy API keys and bioblend. A script is included in the extra-files directory.
python get_tool_yml_from_gi.py --galaxy <my_galaxy_url> --api-key <my_admin_api_key> --output-file <my_tool_list.yml>
Adding a tool_list.yml file to a group_variable files
Group variable files are in the group_vars directory.
If you would like to install tools, you need to reference the tool_list.yml in the group variable file.
We typically place additional files in the
If you would like to add tools to a group that is called metavisitor edit
group_vars/metavisitor and add these lines:
install_tools: true galaxy_tools_tool_list: "extra-files/metavisitor/metavisitor_tool_list.yml"
You can also make sure that workflows are available after running the playbook.
As with tools, place the workflows in
Add these lines to the corresponding group_var file:
galaxy_tools_install_workflows: true galaxy_tools_workflows: - "extra-files/metavisitor/Galaxy-Workflow-create_model.ga" - "extra-files/metavisitor/Galaxy-Workflow-separate_host_and_virus_reads.ga" - "extra-files/metavisitor/Galaxy-Workflow-standart_metavisitor_workflow_(input__clipped_dataset).ga" - "extra-files/metavisitor/Galaxy-Workflow-Metavisitor_Test_case_1-1_Guided.ga" - "extra-files/metavisitor/Galaxy-Workflow-Metavisitor_Test_case_1-2_Guided.ga" - "extra-files/metavisitor/Galaxy-Workflow-Metavisitor_Test_case_1-3_Guided.ga" - "extra-files/metavisitor/Galaxy-Workflow-Meta-visitor__test_case_Nora_virus,_REMAPPING.ga"
Running the playbook
As per usual, run the playbook with an inventory file that maps your target machine to the metavisitor group. If the target is localhost, your inventory file should look ike this:
then run the playbook like so:
ansible-playbook --inventory-file=<your_inventory_file> galaxy.yml