Add support to optionally install iBridges tool

README.md

@@ -32,6 +32,7 @@ Galaxy is configured such that members of the CO that are in the SRAM workspace
 The component takes the following parameters:
 
 * `src_galaxy_version`: set to e.g. `23.0` (default) to control the version of Galaxy that will be installed.
+* `src_ibridges`: Boolean (default: `true`). Whether to enable support for the [iBridges](https://github.com/UtrechtUniversity/galaxy-tools-ibridges) tool for connecting to Yoda and iRODS instances. Implies `src_galaxy_bootstrap`, and adds iBridges to the list of tools to be installed automatically.
 * `src_galaxy_storage_path`: **Interactive parameter**. Default: `/srv/galaxy/datadir`. Path where Galaxy's "mutable data directory" will be located, including the following files:
 
 ```

molecule/default/converge.yml

@@ -8,3 +8,4 @@
   vars:
     src_galaxy_tool_files: "{{ playbook_dir ~ '/molecule/_testfiles/tool_list.yaml.sample' }}"
     src_galaxy_workflow_files: "{{ playbook_dir ~ '/molecule/_testfiles/sample-workflow.ga' }}"
+    src_ibridges: 'true'

templates/galaxy/config/user_preferences_extra_conf.yml.j2

@@ -0,0 +1,14 @@
+preferences:
+{% if _galaxy_ibridges_enabled %}
+    irods_yoda:
+        description: Your YODA account
+        inputs:
+            - name: username
+              label: Username
+              type: text
+              required: True
+            - name: password
+              label: Data Access Password
+              type: secret
+              required: True
+{% endif %}

tools/ibridges.yml

@@ -0,0 +1,8 @@
+---
+tools:
+- name: ibridges
+  owner: maarten.schermer
+  tool_panel_section_id: iBridges
+  tool_shed_url: https://toolshed.g2.bx.psu.edu
+  revisions:
+  - '6194155810b6'  # v0.2

vars/galaxy_vars.yml

@@ -19,6 +19,8 @@ galaxy_client_use_prebuilt: true
 galaxy_systemd_root: true
 galaxy_backup_configfiles: false
 galaxy_config_templates:
+  - src: templates/galaxy/config/user_preferences_extra_conf.yml.j2
+    dest: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
   - src: templates/galaxy/config/job_conf.xml.j2
     dest: "{{ galaxy_config_dir }}/job_conf.xml"
 postgresql_objects_users:
@@ -37,6 +39,7 @@ galaxy_configuration:
     database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
     file_path: "{{ galaxy_mutable_data_dir }}/datasets"
     job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
+    user_preferences_extra_conf_file: "{{ galaxy_config_dir }}/user_preferences_extra_conf.yml"
     interactivetools_enable: "{{ _galaxy_use_interactive_tools }}"
     interactivetools_map: "{{ _galaxy_use_interactive_tools | ternary(gie_proxy_sessions_path, omit) }}"
     galaxy_infrastructure_url: "{{ _galaxy_local_address }}"

vars/src_galaxy_vars.yml

@@ -1,14 +1,19 @@
 # Variables derived from component parameters in ResearchCLoud
+
 _galaxy_bootstrap: "{{ _molecule_idempotence | ternary(false, src_galaxy_bootstrap | default(true, true) | bool ) }}"
-_galaxy_tool_files: "{{ src_galaxy_tool_files | default('') | split(',') | select() }}"  # select() necessary because split on the default '' yields ['']
+_galaxy_ibridges_enabled: "{{ src_ibridges | default(true, true) | bool }}"
+_galaxy_default_tool_files:
+  - path: tools/ibridges.yml
+    enabled: "{{ _galaxy_ibridges_enabled }}"
+_galaxy_default_tool_files_list: "{{ _galaxy_default_tool_files | selectattr('enabled') | map(attribute='path') | list }}"
+_galaxy_tool_files: "{{ src_galaxy_tool_files | default('', true) | split(',') | select() + _galaxy_default_tool_files_list }}"  # select() necessary because split on the default '' yields ['']
 _galaxy_workflow_files: "{{ src_galaxy_workflow_files | default('') | split(',') | select() }}"
 _galaxy_admin_co_group: "{{ src_galaxy_co_admin_group | default('src_co_admin', true) }}"
 _galaxy_custom_repo: "{{ src_galaxy_custom_repo | default('') }}"
 _galaxy_custom_repo_branch: "{{ src_galaxy_custom_repo_branch | default('main', true) }}"
 _galaxy_api_exposed: "{{ src_galaxy_api_exposed | default(true, true) }}"
 _galaxy_use_interactive_tools: "{{ src_galaxy_interactive_tools | default(true, true) | bool }}"
 _galaxy_server_fqdn: "{{ workspace_fqdn | default('localhost', true) }}"
-
 # Note that some component parameters are also used in galaxy_vars.yml:
 # src_galaxy_storage_path
 # src_galaxy_version