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Update container_resolvers_config_file option #4450

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merged 3 commits into from
Oct 23, 2023
Merged

Update container_resolvers_config_file option #4450

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5be2da6
Update container_resolvers_config_file option
pauldg Oct 21, 2023
d743f84
Update in job-destinations
pauldg Oct 23, 2023
75711c1
Update in data-library tutorial
pauldg Oct 23, 2023
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8 changes: 4 additions & 4 deletions topics/admin/tutorials/apptainer/tutorial.md
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Original file line number Diff line number Diff line change
Expand Up @@ -185,7 +185,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil
> tool_data_table_config_path: /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml
> + # Tool Dependencies
> + dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
> + containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> + container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> gravity:
> process_manager: systemd
> galaxy_root: "{{ galaxy_root }}/server"
Expand All @@ -195,7 +195,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil
>
> +galaxy_config_templates:
> + - src: templates/galaxy/config/container_resolvers_conf.yml.j2
> + dest: "{{ galaxy_config.galaxy.containers_resolvers_config_file }}"
> + dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}"
> + - src: templates/galaxy/config/dependency_resolvers_conf.xml
> + dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
> +
Expand Down Expand Up @@ -393,14 +393,14 @@ After finishing the CVMFS tutorial, come back, and do this hands-on.

> <hands-on-title>Optional: Configure Galaxy to use Apptainer containers from CVMFS</hands-on-title>
>
> 1. Edit the `group_vars/galaxyservers.yml` file and add `containers_resolvers_config_file` and `galaxy_singularity_images_cvmfs_path`:
> 1. Edit the `group_vars/galaxyservers.yml` file and add `container_resolvers_config_file` and `galaxy_singularity_images_cvmfs_path`:
> {% raw %}
> ```yaml
> galaxy_singularity_images_cvmfs_path: "/cvmfs/singularity.galaxyproject.org/all/"
> galaxy_config:
> galaxy:
> ...
> containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> ```
> {% endraw %}
>
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2 changes: 1 addition & 1 deletion topics/admin/tutorials/data-library/tutorial.md
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Expand Up @@ -87,7 +87,7 @@ Before we can import local data, we need to configure Galaxy to permit this. Add
> @@ -88,6 +88,9 @@ galaxy_config:
> # Tool Dependencies
> dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
> containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
> + # Data Library Directories
> + library_import_dir: /libraries/admin
> + user_library_import_dir: /libraries/user
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2 changes: 1 addition & 1 deletion topics/admin/tutorials/job-destinations/tutorial.md
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Expand Up @@ -652,7 +652,7 @@ Such form elements can be added to tools without modifying each tool's configura
> slow_query_log_threshold: 5
> enable_per_request_sql_debugging: true
> @@ -137,6 +146,8 @@ galaxy_config_templates:
> dest: "{{ galaxy_config.galaxy.containers_resolvers_config_file }}"
> dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}"
> - src: templates/galaxy/config/dependency_resolvers_conf.xml
> dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
> + - src: templates/galaxy/config/job_resource_params_conf.xml.j2
Expand Down
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