Nate finds all my missing J2s.

Co-Authored-By: Nate Coraor <[email protected]>

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
 >    <job_conf>
@@ -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 `<destination>` 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 @@
 >     <job_conf>
 >         <plugins workers="4">
@@ -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
 >            <destination id="slurm-2c" runner="slurm">
->                <param id="nativeSpecification">--nodes=1 --ntasks=1 --cpus-per-task=4</param>
+>                <param id="nativeSpecification">--nodes=1 --ntasks=1 --cpus-per-task=2</param>
 >            </destination>
 >    ```
 > 2. Then, map the new tool to the new destination using the tool ID (`<tool id="testing">`) and destination id (`<destination id="slurm-2c">`) by adding a new section to the job config, `<tools>`, 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
 >    <parameters>
@@ -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`: `<resources>`. 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`: `<resources>`. 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
 >        <resources>

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
 >    <toolbox monitor="true">
@@ -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
 >    <job_conf>
@@ -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.
 >
 >    <br/>
 >

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
 >    <?xml version="1.0"?>
@@ -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"