diff --git a/topics/admin/tutorials/apptainer/tutorial.md b/topics/admin/tutorials/apptainer/tutorial.md index 210c367dfebc34..e7c5fb1727c7af 100644 --- a/topics/admin/tutorials/apptainer/tutorial.md +++ b/topics/admin/tutorials/apptainer/tutorial.md @@ -178,7 +178,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -72,6 +72,9 @@ galaxy_config: +> @@ -75,6 +75,9 @@ galaxy_config: > tus_upload_store: "{{ galaxy_tus_upload_store }}" > # CVMFS > 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 @@ -188,7 +188,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil > gravity: > process_manager: systemd > galaxy_root: "{{ galaxy_root }}/server" -> @@ -111,6 +114,12 @@ galaxy_config_files: +> @@ -114,6 +117,12 @@ galaxy_config_files: > - src: files/galaxy/themes.yml > dest: "{{ galaxy_config.galaxy.themes_config_file }}" > diff --git a/topics/admin/tutorials/celery/tutorial.md b/topics/admin/tutorials/celery/tutorial.md index 1b8d52bb05f061..8aa280f9517917 100644 --- a/topics/admin/tutorials/celery/tutorial.md +++ b/topics/admin/tutorials/celery/tutorial.md @@ -148,7 +148,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -279,3 +279,7 @@ rabbitmq_users: +> @@ -282,3 +282,7 @@ rabbitmq_users: > # TUS > galaxy_tusd_port: 1080 > galaxy_tus_upload_store: /data/tus @@ -247,7 +247,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -266,6 +266,7 @@ rabbitmq_config: +> @@ -269,6 +269,7 @@ rabbitmq_config: > > rabbitmq_vhosts: > - /pulsar/pulsar_au @@ -255,7 +255,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > > rabbitmq_users: > - user: admin -> @@ -275,6 +276,13 @@ rabbitmq_users: +> @@ -278,6 +279,13 @@ rabbitmq_users: > - user: pulsar_au > password: "{{ vault_rabbitmq_password_vhost }}" > vhost: /pulsar/pulsar_au @@ -298,7 +298,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -291,3 +291,22 @@ galaxy_tus_upload_store: /data/tus +> @@ -294,3 +294,22 @@ galaxy_tus_upload_store: /data/tus > #Redis > galaxy_additional_venv_packages: > - redis @@ -372,7 +372,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -127,6 +127,11 @@ galaxy_config: +> @@ -130,6 +130,11 @@ galaxy_config: > preload: true > celery: > concurrency: 2 @@ -393,7 +393,7 @@ First we need to add our new Ansible Roles to the `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -108,6 +108,11 @@ galaxy_config: +> @@ -111,6 +111,11 @@ galaxy_config: > # Data Library Directories > library_import_dir: /libraries/admin > user_library_import_dir: /libraries/user diff --git a/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md b/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md index de2f984aa631f7..375c5a175d5890 100644 --- a/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md +++ b/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md @@ -125,7 +125,7 @@ be taken into consideration when choosing where to run jobs and what parameters > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -191,6 +191,16 @@ nginx_ssl_role: usegalaxy_eu.certbot +> @@ -194,6 +194,16 @@ nginx_ssl_role: usegalaxy_eu.certbot > nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem > nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-www-data.pem > diff --git a/topics/admin/tutorials/customization/tutorial.md b/topics/admin/tutorials/customization/tutorial.md index 9e07515b1c65e1..61d6b3db2dc0bc 100644 --- a/topics/admin/tutorials/customization/tutorial.md +++ b/topics/admin/tutorials/customization/tutorial.md @@ -30,6 +30,7 @@ Customizing your Galaxy instance makes it more recognizable at a glance, and can This tutorial will teach you three basic customizations you can make to Galaxy: - Setting a brand text + - Setting the contact information - Adding a custom welcome page - Customizing the masthead using themes @@ -85,6 +86,35 @@ It is an easy way to set your instance apart, and make it more identifiable. > ![screenshot of fictional "Galaxy Mars" start page, with the brand text set to "Mars"](images/galaxy-mars-brand.png "Your Galaxy start page should now look something like this") {: .hands_on} +## Configuring Support + +The Galaxy Help Site (https://help.galaxyproject.org) receives a lot of user support questions, sometimes for Galaxies that we do not manage. Including support information inside your Galaxy can help users find the right place to ask about issues with tools or quotas! + +> Adding Support Information +> +> 1. Open your `group_vars/galaxyserers.yml` and the following option under `galaxy_config.galaxy`: +> +> {% raw %} +> ```diff +> --- a/group_vars/galaxyservers.yml +> +++ b/group_vars/galaxyservers.yml +> @@ -35,6 +35,9 @@ galaxy_config: +> # Branding +> brand: Mars 🚀 +> logo_src: "https://training.galaxyproject.org/training-material/topics/admin/tutorials/customization/images/logo.png" +> + # Support +> + support_url: "https://example.org/support" +> + terms_url: "https://example.org/terms-of-service" +> # Main Configuration +> admin_users: +> - admin@example.org +> {% endraw %} +> ``` +> {: data-commit="Add support information"} +> +> Ideally this would point to a support URL and a terms of service that are appropriate to *your* deployment of Galaxy. You could, for instance, add a page on your group's blog with the appropriate contents of who should be contacted in case of issue, their email or a ticketing system. These options will help users from your site find you when they need help. +{: .hands_on} + ## Custom Welcome Page The welcome page is an html document embedded in Galaxy's start page. @@ -101,7 +131,7 @@ This page can be used to communicate what your instance is about, and share news > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -93,6 +93,10 @@ galaxy_config: +> @@ -96,6 +96,10 @@ galaxy_config: > - job-handlers > - workflow-schedulers > @@ -208,10 +238,10 @@ You can even offer several options, to allow users to switch to the default if t > brand: Mars 🚀 > logo_src: "https://training.galaxyproject.org/training-material/topics/admin/tutorials/customization/images/logo.png" > + themes_config_file: "{{ galaxy_config_dir }}/themes.yml" -> # Main Configuration -> admin_users: -> - admin@example.org -> @@ -97,6 +98,10 @@ galaxy_config_files_public: +> # Support +> support_url: "https://example.org/support" +> terms_url: "https://example.org/terms-of-service" +> @@ -100,6 +101,10 @@ galaxy_config_files_public: > - src: files/galaxy/welcome.html > dest: "{{ galaxy_mutable_config_dir }}/welcome.html" > diff --git a/topics/admin/tutorials/cvmfs/tutorial.md b/topics/admin/tutorials/cvmfs/tutorial.md index ff583d45423b97..c95e304534d252 100644 --- a/topics/admin/tutorials/cvmfs/tutorial.md +++ b/topics/admin/tutorials/cvmfs/tutorial.md @@ -506,7 +506,7 @@ Now all we need to do is tell Galaxy how to find it! This tutorial assumes that > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -70,6 +70,8 @@ galaxy_config: +> @@ -73,6 +73,8 @@ galaxy_config: > # TUS > galaxy_infrastructure_url: "https://{{ inventory_hostname }}" > tus_upload_store: "{{ galaxy_tus_upload_store }}" diff --git a/topics/admin/tutorials/data-library/tutorial.md b/topics/admin/tutorials/data-library/tutorial.md index 9de22f93a39b7e..5d17f2b6fc1898 100644 --- a/topics/admin/tutorials/data-library/tutorial.md +++ b/topics/admin/tutorials/data-library/tutorial.md @@ -84,7 +84,7 @@ Before we can import local data, we need to configure Galaxy to permit this. Add > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -88,6 +88,9 @@ galaxy_config: +> @@ -91,6 +91,9 @@ galaxy_config: > # Tool Dependencies > dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml" > container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml" diff --git a/topics/admin/tutorials/ftp/tutorial.md b/topics/admin/tutorials/ftp/tutorial.md index 055646e0ac096d..961881ae7ec139 100644 --- a/topics/admin/tutorials/ftp/tutorial.md +++ b/topics/admin/tutorials/ftp/tutorial.md @@ -111,7 +111,7 @@ If the terms "Ansible", "role" and "playbook" mean nothing to you, please checko > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -207,11 +207,13 @@ certbot_environment: staging +> @@ -210,11 +210,13 @@ certbot_environment: staging > certbot_well_known_root: /srv/nginx/_well-known_root > certbot_share_key_users: > - www-data @@ -137,7 +137,7 @@ If the terms "Ansible", "role" and "playbook" mean nothing to you, please checko > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -119,6 +119,9 @@ galaxy_config: +> @@ -122,6 +122,9 @@ galaxy_config: > sentry_dsn: "{{ vault_galaxy_sentry_dsn }}" > sentry_traces_sample_rate: 0.5 > error_report_file: "{{ galaxy_config_dir }}/error_reports_file.yml" @@ -159,7 +159,7 @@ If the terms "Ansible", "role" and "playbook" mean nothing to you, please checko > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -363,3 +363,24 @@ telegraf_plugins_extra: +> @@ -366,3 +366,24 @@ telegraf_plugins_extra: > tiaas_dir: /srv/tiaas > tiaas_admin_user: admin > tiaas_admin_pass: changeme diff --git a/topics/admin/tutorials/job-destinations/tutorial.md b/topics/admin/tutorials/job-destinations/tutorial.md index 79eeea118fa450..236a4972cf1fd1 100644 --- a/topics/admin/tutorials/job-destinations/tutorial.md +++ b/topics/admin/tutorials/job-destinations/tutorial.md @@ -107,7 +107,7 @@ To demonstrate a real-life scenario and {TPV}'s role in it, let's plan on settin > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -152,6 +152,9 @@ galaxy_config_templates: +> @@ -155,6 +155,9 @@ galaxy_config_templates: > galaxy_extra_dirs: > - /data > @@ -197,7 +197,7 @@ And of course, Galaxy has an Ansible Role for that. > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -135,6 +135,8 @@ galaxy_config: +> @@ -138,6 +138,8 @@ galaxy_config: > - job-handlers > - workflow-schedulers > @@ -206,7 +206,7 @@ And of course, Galaxy has an Ansible Role for that. > galaxy_config_files_public: > - src: files/galaxy/welcome.html > dest: "{{ galaxy_mutable_config_dir }}/welcome.html" -> @@ -151,6 +153,11 @@ galaxy_config_templates: +> @@ -154,6 +156,11 @@ galaxy_config_templates: > > galaxy_extra_dirs: > - /data @@ -297,7 +297,7 @@ We want our tool to run with more than one core. To do this, we need to instruct > tools: > - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc > environment: local_env -> @@ -144,6 +128,8 @@ galaxy_config_files_public: +> @@ -147,6 +131,8 @@ galaxy_config_files_public: > galaxy_config_files: > - src: files/galaxy/themes.yml > dest: "{{ galaxy_config.galaxy.themes_config_file }}" @@ -639,7 +639,7 @@ Such form elements can be added to tools without modifying each tool's configura > > galaxy_config: > galaxy: -> @@ -56,6 +64,7 @@ galaxy_config: +> @@ -59,6 +67,7 @@ galaxy_config: > object_store_store_by: uuid > id_secret: "{{ vault_id_secret }}" > job_config: "{{ galaxy_job_config }}" # Use the variable we defined above @@ -647,7 +647,7 @@ Such form elements can be added to tools without modifying each tool's configura > # SQL Performance > slow_query_log_threshold: 5 > enable_per_request_sql_debugging: true -> @@ -137,6 +146,8 @@ galaxy_config_templates: +> @@ -140,6 +149,8 @@ galaxy_config_templates: > dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}" > - src: templates/galaxy/config/dependency_resolvers_conf.xml > dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" diff --git a/topics/admin/tutorials/monitoring/tutorial.md b/topics/admin/tutorials/monitoring/tutorial.md index 559c3799922b4c..53146d8196c086 100644 --- a/topics/admin/tutorials/monitoring/tutorial.md +++ b/topics/admin/tutorials/monitoring/tutorial.md @@ -375,7 +375,7 @@ Setting up Telegraf is again very simple. We just add a single role to our playb > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -327,3 +327,12 @@ flower_ui_users: +> @@ -330,3 +330,12 @@ flower_ui_users: > > flower_environment_variables: > GALAXY_CONFIG_FILE: "{{ galaxy_config_file }}" @@ -402,7 +402,7 @@ Setting up Telegraf is again very simple. We just add a single role to our playb > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -113,6 +113,9 @@ galaxy_config: +> @@ -116,6 +116,9 @@ galaxy_config: > celery_conf: > result_backend: "redis://localhost:6379/0" > enable_celery_tasks: true @@ -798,7 +798,7 @@ You can run the playbook now, or wait until you have configured Telegraf below: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -339,3 +339,10 @@ telegraf_plugins_extra: +> @@ -342,3 +342,10 @@ telegraf_plugins_extra: > - service_address = ":8125" > - metric_separator = "." > - allowed_pending_messages = 10000 diff --git a/topics/admin/tutorials/pulsar/tutorial.md b/topics/admin/tutorials/pulsar/tutorial.md index 925eb1cfd54b0e..6f85e6de0772be 100644 --- a/topics/admin/tutorials/pulsar/tutorial.md +++ b/topics/admin/tutorials/pulsar/tutorial.md @@ -271,7 +271,7 @@ More information about the rabbitmq ansible role can be found [in the repository > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -171,8 +171,11 @@ certbot_environment: staging +> @@ -174,8 +174,11 @@ certbot_environment: staging > certbot_well_known_root: /srv/nginx/_well-known_root > certbot_share_key_users: > - www-data @@ -283,7 +283,7 @@ More information about the rabbitmq ansible role can be found [in the repository > certbot_domains: > - "{{ inventory_hostname }}" > certbot_agree_tos: --agree-tos -> @@ -222,6 +225,47 @@ slurm_config: +> @@ -225,6 +228,47 @@ slurm_config: > SelectType: select/cons_res > SelectTypeParameters: CR_CPU_Memory # Allocate individual cores/memory instead of entire node > diff --git a/topics/admin/tutorials/reports/tutorial.md b/topics/admin/tutorials/reports/tutorial.md index 9b53a444014b1d..663ac16cd478e7 100644 --- a/topics/admin/tutorials/reports/tutorial.md +++ b/topics/admin/tutorials/reports/tutorial.md @@ -82,7 +82,7 @@ The reports application is included with the Galaxy codebase and this tutorial a > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -148,6 +148,11 @@ galaxy_config: +> @@ -151,6 +151,11 @@ galaxy_config: > pools: > - job-handlers > - workflow-schedulers @@ -94,7 +94,7 @@ The reports application is included with the Galaxy codebase and this tutorial a > > galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml" > -> @@ -168,6 +173,8 @@ galaxy_config_templates: +> @@ -171,6 +176,8 @@ galaxy_config_templates: > dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}" > - src: templates/galaxy/config/job_resource_params_conf.xml.j2 > dest: "{{ galaxy_config.galaxy.job_resource_params_file }}" diff --git a/topics/admin/tutorials/sentry/tutorial.md b/topics/admin/tutorials/sentry/tutorial.md index eededae764eda3..3dc4954442316a 100644 --- a/topics/admin/tutorials/sentry/tutorial.md +++ b/topics/admin/tutorials/sentry/tutorial.md @@ -255,7 +255,7 @@ First we need to add our new Ansible role to `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -216,6 +216,7 @@ nginx_servers: +> @@ -219,6 +219,7 @@ nginx_servers: > - redirect-ssl > nginx_ssl_servers: > - galaxy @@ -300,7 +300,7 @@ First we need to add our new Ansible role to `requirements.yml`: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -116,6 +116,8 @@ galaxy_config: +> @@ -119,6 +119,8 @@ galaxy_config: > # Monitoring > statsd_host: localhost > statsd_influxdb: true @@ -434,7 +434,7 @@ In addition to sending logging errors to Sentry you can also collect failing too > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -118,6 +118,7 @@ galaxy_config: +> @@ -121,6 +121,7 @@ galaxy_config: > statsd_influxdb: true > sentry_dsn: "{{ vault_galaxy_sentry_dsn }}" > sentry_traces_sample_rate: 0.5 @@ -442,7 +442,7 @@ In addition to sending logging errors to Sentry you can also collect failing too > gravity: > process_manager: systemd > galaxy_root: "{{ galaxy_root }}/server" -> @@ -170,6 +171,8 @@ galaxy_config_files: +> @@ -173,6 +174,8 @@ galaxy_config_files: > dest: "{{ galaxy_config.galaxy.themes_config_file }}" > - src: files/galaxy/config/tpv_rules_local.yml > dest: "{{ tpv_mutable_dir }}/tpv_rules_local.yml" @@ -451,7 +451,7 @@ In addition to sending logging errors to Sentry you can also collect failing too > > galaxy_config_templates: > - src: templates/galaxy/config/container_resolvers_conf.yml.j2 -> @@ -191,6 +194,7 @@ tpv_privsep: true +> @@ -194,6 +197,7 @@ tpv_privsep: true > > galaxy_local_tools: > - testing.xml diff --git a/topics/admin/tutorials/tiaas/tutorial.md b/topics/admin/tutorials/tiaas/tutorial.md index 3529ec273616a9..8d6acb5e46c6b8 100644 --- a/topics/admin/tutorials/tiaas/tutorial.md +++ b/topics/admin/tutorials/tiaas/tutorial.md @@ -91,7 +91,7 @@ This tutorial will go cover how to set up such a service on your own Galaxy serv > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -346,3 +346,8 @@ telegraf_plugins_extra: +> @@ -349,3 +349,8 @@ telegraf_plugins_extra: > - timeout = "10s" > - data_format = "influx" > - interval = "15s" diff --git a/topics/admin/tutorials/tus/tutorial.md b/topics/admin/tutorials/tus/tutorial.md index 5d9904b4aacb31..30cec6b5ae6e7b 100644 --- a/topics/admin/tutorials/tus/tutorial.md +++ b/topics/admin/tutorials/tus/tutorial.md @@ -80,7 +80,7 @@ To allow your user to upload via TUS, you will need to: > ```diff > --- a/group_vars/galaxyservers.yml > +++ b/group_vars/galaxyservers.yml -> @@ -67,6 +67,9 @@ galaxy_config: +> @@ -70,6 +70,9 @@ galaxy_config: > # Tool security > outputs_to_working_directory: true > new_user_dataset_access_role_default_private: true # Make datasets private by default @@ -90,7 +90,7 @@ To allow your user to upload via TUS, you will need to: > gravity: > process_manager: systemd > galaxy_root: "{{ galaxy_root }}/server" -> @@ -87,6 +90,10 @@ galaxy_config: +> @@ -90,6 +93,10 @@ galaxy_config: > celery: > concurrency: 2 > loglevel: DEBUG @@ -101,7 +101,7 @@ To allow your user to upload via TUS, you will need to: > handlers: > handler: > processes: 2 -> @@ -156,3 +163,7 @@ nginx_conf_http: +> @@ -159,3 +166,7 @@ nginx_conf_http: > nginx_ssl_role: usegalaxy_eu.certbot > nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem > nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-www-data.pem