diff --git a/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md b/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md index cb96cfad521cc6..5451da7f2ada4f 100644 --- a/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md +++ b/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md @@ -77,12 +77,12 @@ be taken into consideration when choosing where to run jobs and what parameters > ansible-galaxy install -p roles -r requirements.yml > ``` > -> 4. Add the following roles to the *beginning* of your roles section in your `galaxy.yml` playbook: +> 3. Add the following roles to the *beginning* of your roles section in your `galaxy.yml` playbook: > > - `galaxyproject.repos` > - `galaxyproject.slurm` > -> 5. Add the slurm variables to your `group_vars/galaxyservers.yml`: +> 4. Add the slurm variables to your `group_vars/galaxyservers.yml`: > > ``` > # slurm @@ -296,7 +296,7 @@ At the top of the stack sits Galaxy. Galaxy must now be configured to use the cl > > If the folder does not exist, create `templates/galaxy/config` next to your `galaxy.yml` playbook (`mkdir -p templates/galaxy/config/`). > -> Create `templates/galaxy/config/job_conf.xml` with the following contents: +> Create `templates/galaxy/config/job_conf.xml.j2` with the following contents: > > ```xml > @@ -311,14 +311,14 @@ At the top of the stack sits Galaxy. Galaxy must now be configured to use the cl > > > ### {% icon comment %} Note > > -> > Depending on the order in which you are completing this tutorial in relation to other tutorials, you may have already created the `job_conf.xml` file, as well as defined `galaxy_config_templates` and set the `job_config_file` option in `galaxy_config` (step 4). If this is the case, be sure to **merge the changes in this section with your existing playbook**. +> > Depending on the order in which you are completing this tutorial in relation to other tutorials, you may have already created the `job_conf.xml.j2` file, as well as defined `galaxy_config_templates` and set the `job_config_file` option in `galaxy_config` (step 4). If this is the case, be sure to **merge the changes in this section with your existing playbook**. > {: .comment} > > 3. Next, we need to configure the Slurm job runner. First, we instruct Galaxy's job handlers to load the Slurm job runner plugin, and set the Slurm job submission parameters. A job runner plugin definition must have the `id`, `type`, and `load` attributes. Then we add a basic destination with no parameters, Galaxy will do the equivalent of submitting a job as `sbatch /path/to/job_script.sh`. Note that we also need to set a default destination now that more than one destination is defined. In a `` tag, the `id` attribute is a unique identifier for that destination and the `runner` attribute must match the `id` of a defined plugin: > > ```diff -> --- templates/galaxy/config/job_conf.xml.old -> +++ templates/galaxy/config/job_conf.xml +> --- templates/galaxy/config/job_conf.xml.j2.old +> +++ templates/galaxy/config/job_conf.xml.j2 > @@ -1,8 +1,9 @@ > > @@ -352,7 +352,7 @@ At the top of the stack sits Galaxy. Galaxy must now be configured to use the cl > ```yaml > galaxy_config_templates: > # ... possible existing config file definitions -> - src: templates/galaxy/config/job_conf.xml +> - src: templates/galaxy/config/job_conf.xml.j2 > dest: "{{ galaxy_job_config_file }}" > ``` > {% endraw %} @@ -537,11 +537,11 @@ We want our tool to run with more than one core. To do this, we need to instruct > ### {% icon hands_on %} Hands-on: Allocating more resources > -> 1. Edit your `templates/galaxy/config/job_conf.xml` and add the following destination: +> 1. Edit your `templates/galaxy/config/job_conf.xml.j2` and add the following destination: > > ```xml > -> --nodes=1 --ntasks=1 --cpus-per-task=4 +> --nodes=1 --ntasks=1 --cpus-per-task=2 > > ``` > 2. Then, map the new tool to the new destination using the tool ID (``) and destination id (``) by adding a new section to the job config, ``, below the destinations: @@ -726,7 +726,7 @@ Such form elements can be added to tools without modifying each tool's configura > ### {% icon hands_on %} Hands-on: Configuring a Resource Selector > -> 1. Create and open `templates/galaxy/config/job_resource_params_conf.xml` +> 1. Create and open `templates/galaxy/config/job_resource_params_conf.xml.j2` > > ```xml > @@ -751,11 +751,11 @@ Such form elements can be added to tools without modifying each tool's configura > ... > galaxy_config_templates: > ... -> - src: templates/galaxy/config/job_resource_params_conf.xml +> - src: templates/galaxy/config/job_resource_params_conf.xml.j2 > dest: {% raw %}"{{ galaxy_config.galaxy.job_resource_params_file }}"{% endraw %} > ``` > -> 3. Next, we define a new section in `job_conf.xml`: ``. This groups together parameters that should appear together on a tool form. Add the following section to your `templates/galaxy/config/job_conf.xml`: +> 3. Next, we define a new section in `job_conf.xml`: ``. This groups together parameters that should appear together on a tool form. Add the following section to your `templates/galaxy/config/job_conf.xml.j2`: > > ```xml > diff --git a/topics/admin/tutorials/interactive-tools/tutorial.md b/topics/admin/tutorials/interactive-tools/tutorial.md index 5f67f8b9593278..a20a224c5af56b 100644 --- a/topics/admin/tutorials/interactive-tools/tutorial.md +++ b/topics/admin/tutorials/interactive-tools/tutorial.md @@ -459,7 +459,7 @@ A few Interactive Tool wrappers are provided with Galaxy, but they are [commente > > If the folder does not exist, create `templates/galaxy/config` next to your `galaxy.yml` (`mkdir -p templates/galaxy/config/`) > -> Create `templates/galaxy/config/tool_conf_interactive.xml` with the following contents: +> Create `templates/galaxy/config/tool_conf_interactive.xml.j2` with the following contents: > > ```xml > @@ -471,7 +471,7 @@ A few Interactive Tool wrappers are provided with Galaxy, but they are [commente > > 2. We need to modify `job_conf.xml` to instruct Galaxy on how run Interactive Tools (and specifically, how to run them in Docker). We will begin with a basic job conf: > -> Create `templates/galaxy/config/job_conf.xml` with the following contents: +> Create `templates/galaxy/config/job_conf.xml.j2` with the following contents: > > ```xml > @@ -485,7 +485,7 @@ A few Interactive Tool wrappers are provided with Galaxy, but they are [commente > ``` > > > ### {% icon comment %} Note -> > Depending on the order in which you are completing this tutorial in relation to other tutorials, you may have already created the `job_conf.xml` file, as well as defined `galaxy_config_templates` and set the `job_config_file` option in `galaxy_config` (step 4). If this is the case, be sure to **merge the changes in this section with your existing playbook**. +> > Depending on the order in which you are completing this tutorial in relation to other tutorials, you may have already created the `job_conf.xml.j2` file, as well as defined `galaxy_config_templates` and set the `job_config_file` option in `galaxy_config` (step 4). If this is the case, be sure to **merge the changes in this section with your existing playbook**. > {: .comment} > > 3. Next, we need to configure the interactive tools destination. First, we explicitly set the destination to the default `local` destination since there will now be two destinations defined. Then we add a destination for submitting jobs as docker containers using the [advanced sample job configuration][job-conf-docker] as a guide. Finally, use the [EtherCalc GxIT's][ethercalc-tool-wrapper] tool ID to route executions of the EtherCalc GxIT to the newly created destination: @@ -521,7 +521,7 @@ A few Interactive Tool wrappers are provided with Galaxy, but they are [commente > > {% raw %} > ```yaml -> galaxy_tool_config_templates: +> galaxy_tool_config_files: > - "{{ galaxy_server_dir }}/config/tool_conf.xml.sample" > - "{{ galaxy_config_dir }}/tool_conf_interactive.xml" > ``` @@ -548,9 +548,9 @@ A few Interactive Tool wrappers are provided with Galaxy, but they are [commente > ```yaml > galaxy_config_templates: > # ... possible existing config file definitions -> - src: templates/galaxy/config/tool_conf_interactive.xml +> - src: templates/galaxy/config/tool_conf_interactive.xml.j2 > dest: "{{ galaxy_config_dir }}/tool_conf_interactive.xml" -> - src: templates/galaxy/config/job_conf.xml +> - src: templates/galaxy/config/job_conf.xml.j2 > dest: "{{ galaxy_job_config_file }}" > ``` > {% endraw %} @@ -664,7 +664,7 @@ Because we want to maintain dataset privacy, Pulsar is the better choice here. A > ``` > {% endraw %} > -> 2. Modify the job configuration file, `templates/galaxy/config/job_conf.xml`, to configure Interactive Tools to use the embedded Pulsar runner. +> 2. Modify the job configuration file, `templates/galaxy/config/job_conf.xml.j2`, to configure Interactive Tools to use the embedded Pulsar runner. > >
> diff --git a/topics/admin/tutorials/job-metrics/tutorial.md b/topics/admin/tutorials/job-metrics/tutorial.md index e9a86af4f58471..18d2ead2c82208 100644 --- a/topics/admin/tutorials/job-metrics/tutorial.md +++ b/topics/admin/tutorials/job-metrics/tutorial.md @@ -53,7 +53,7 @@ These include very basic submission parameters. We want more information! > ### {% icon hands_on %} Hands-on: Setting up the job metrics file > -> 1. Create the file `templates/galaxy/config/job_metrics_conf.xml` with the following contents: +> 1. Create the file `templates/galaxy/config/job_metrics_conf.xml.j2` with the following contents: > > ```xml > @@ -95,7 +95,7 @@ These include very basic submission parameters. We want more information! > gie_proxy_sessions_path: "{{ galaxy_mutable_data_dir }}/interactivetools_map.sqlite" > > galaxy_config_templates: -> + - src: templates/galaxy/config/job_metrics_conf.xml +> + - src: templates/galaxy/config/job_metrics_conf.xml.j2 > + dest: "{{ galaxy_job_metrics_config_file }}" > - src: templates/galaxy/config/tool_conf_interactive.xml > dest: "{{ galaxy_config_dir }}/tool_conf_interactive.xml"