Installing tools and workflows¶

This playbook includes the ansible-galaxy-tools role which can be used to install tools and workflows into galaxy instances using the bioblend API.

Importantly, in the latest GalaxyKickStart version (v20.05), tool installation is performed using a separate run of ansible-playbook, typically:

# these steps have should have already been performed

# ansible-galaxy install -r requirements_roles.yml -p roles/
# ansible-playbook -i inventory_files/galaxy-kickstart galaxy.yml

ansible-playbook -i inventory_files/galaxy-kickstart galaxy_tool_install.yml

Note that this is during the galaxy_tool_install.yml ansible play that a Galaxy admin user account is created with the credentials admin@galaxy.org:artbio2020

Creating a tool_list.yml file¶

Before running the galaxy_tool_install.yml playbook script as shown above, you need to prepare a tool_list.yml file with a list of tools in yaml format and with the following example content:

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/

If the revisions key is empty, the latest available in the Galaxy toolshed revision will be installed.

The tool_panel_section_label key sets the tool panel section where the tools will show up in the Galaxy tool bar.

Another example of a a tool list can be found in here

Obtaining a tool_list.yml file from a running Galaxy server¶

You can also retrieve the list of tools running in a specific Galaxy instance using the ephemeris script workflow-to-tools.

First Install ephememeris using pip
```
pip install ephemeris
```

This will bring several scripts in your pip environment:

run-data-managers --help
shed-tools install --help
shed-tools update --help
workflow-install --help
setup-data-libraries --help
get-tool-list --help
workflow-to-tools --help

Use the ephemeris get-tool-list to retrieve a yml list of tools installed in the Galaxy server using the command:

get-tool-list -g https://usegalaxy.org -u <main galaxy username> -p <user password> --get_data_managers -o main_tools_list.yml

Obtaining a tool_list.yml file from a workflow.ga galaxy file.¶

You can also retrieve a list of tools used in one or more workflow galaxy files (.ga extension).

These .ga files can be obtain from Galaxy server instances (menu "download workflow file") or other repositories

Use the ephemeris workflow-to-tools to retrieve a yml list of tools using the command:
```
workflow-to-tools -w <Galaxy-Workflow-File.ga> -l <menu_label> -o <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 extra-files/<hostname>/<hostname>_tool_list.yml file.

For instance, 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"

Installing workflows¶

You can also add workflows in the Galaxy server modified by playbook script galaxy_tool_install.yml.

As with tools, place the workflows in extra-files/<hostname>/<hostname><workflow_name>.ga and add these lines to the corresponding group_var file:

galaxy_tools_install_workflows: true
galaxy_tools_workflows:
  - "extra-files/metavisitor/my_workflow_1.ga"
  - "extra-files/metavisitor/my_workflow_2.ga"
  - "extra-files/metavisitor/my_workflow_3.ga"

Running the playbook¶

As mentioned earlier, after these preparation steps, you can run the playbook script galaxy_tool_install.yml with an inventory file that maps your target machine to the metavisitor group (in this example).

If the target is localhost, your inventory file should look like this:

[metavisitor]
localhost

then run the playbook like so:

ansible-playbook -i inventory_files/galaxy-kickstart galaxy_tool_install.yml