Advanced customisation of a Galaxy instance

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---

# Advanced customisation of a Galaxy instance

<div class="contributors-line">
		
	
<ul class="text-list">
			
			<li>
				
  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
  
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  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
  
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  <a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-martenson"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" />
    Martin Čech</a>
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---

### Setup

We are going to use a prebuilt virtual machine image for this session.

From the given USB stick, please:

* Copy and install VirtualBox (or [download](https://www.virtualbox.org/wiki/Downloads)) if you do not have it already.
* Copy the Planemo machine image - file `latest.ova` or [download](https://images.galaxyproject.org/planemo/).

---

## Galaxy's frontend

JavaScript sources and CSS sources are in the `$GALAXY_ROOT/client` folder.

Whenever you make changes there, you will need to re-build Galaxy's frontend with:

```console
$ cd $GALAXY_ROOT
$ make client
```

This requires [Node](https://nodejs.org/).

---

### Translation and localisation 1/2

The language for labels used in the JS source code is English, but can be wrapped in `l()` which makes it translatable.

```javascript
_l( 'Help' )
```

* There is a script [client/galaxy/scripts/nls/locale.js](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/nls/locale.js) that defines all translatable labels. By default without a translation.

```javascript
"Analyze Data" :
    false,
```

* There is a folder [client/galaxy/scripts/nls/](https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/nls) that contains all available localisations.
```
"Analyze Data" :
    "Analyse de données",
```

---

### Translation and localisation 2/2

When a user's browser locale or language is set to a known translation, it will be used instead of the default. If a translation is not available for a string, it will appear in English.

---

### How to modify the menu

Open the [client/galaxy/scripts/layout/menu.js](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/layout/menu.js)

```javascript
var helpTab = {
          id              : 'help',
          title           : _l('Help'),
          tooltip         : _l('Support, contact, and community'),
          menu            : [{
                  title   : _l('Support'),
                  url     : options.support_url,
                  target  : '_blank'
              },{
                  title   : _l('Search'),
                  url     : options.search_url,
                  target  : '_blank'
```

---

## Configuration tweaks

Plenty of customisation can be achieved using settings in the main configuration file [galaxy.yml](https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample)

---

### Tool Panel configuration

* How the tool panel looks like is decided in a file called `integrated_tool_panel.xml`.
* By default it resides in Galaxy's root folder.
* If missing it is generated from all other tool config files during startup.
* Modify it if you want to reorder tools or move sections.

---

### Tool panel labels

You can add `<tool labels="updated" />` to achieve:

![tool panel labels](../../images/toolpanel_labels.png)

---

### Tool Panel search configuration 1/2

The tool panel search uses a pre-built index that is compiled during Galaxy
boot. You can tweak tool panel search by configuring boosts in `galaxy.yml`.

```ini
tool_name_boost: 9
tool_section_boost: 3
tool_description_boost: 2
tool_label_boost: 1
tool_stub_boost: 5
tool_help_boost: 0.5
```

You can also manipulate the number of tools returned for any query by changing
the `tool_search_limit`. This will display more or fewer tools for any given
query.

---

### Tool Panel search configuration 2/2

```ini
# Enable/ disable Ngram-search for tools. It makes tool
# search results tolerant for spelling mistakes in the query
# by dividing the query into multiple ngrams and search for
# each ngram
tool_enable_ngram_search: true

# Set minimum and maximum sizes of ngrams
tool_ngram_minsize: 3
tool_ngram_maxsize: 5
```

---

### Log level configuration

```ini
# Verbosity of console log messages.
log_level: DEBUG
```

These are [python logging levels](https://docs.python.org/2/library/logging.html#logging-levels).

![log levels](../../images/log_levels.png)

---

### Help menu

```ini
# The URL linked by the "Wiki" link in the "Help" menu.
wiki_url: https://galaxyproject.org/

# The URL linked by the "Support" link in the "Help" menu.
support_url: https://galaxyproject.org/support

# The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
#citation_url: https://galaxyproject.org/citing-galaxy

# The URL linked by the "Search" link in the "Help" menu.
#search_url: https://galaxyproject.org/search/

# The URL linked by the "Mailing Lists" link in the "Help" menu.
#mailing_lists_url: https://galaxyproject.org/mailing-lists

# The URL linked by the "Videos" link in the "Help" menu.
#screencasts_url: https://vimeo.com/galaxyproject

# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
# as on the user registration and login forms and in the activation emails.
#terms_url: None
```

---

### Brand and welcome

```ini
# Append "/{brand}" to the "Galaxy" text in the masthead.
brand: GenOuest
```

![brand](../../images/brand.png)

```ini
# The URL linked by the "Galaxy/brand" text.
logo_url: /

# The URL of the page to display in Galaxy's middle pane when loaded.  This can
# be an absolute or relative URL.
welcome_url: /static/welcome.html
```

---

### Email configuration

```ini
error_email_to: marten+error@bx.psu.edu
activation_email: marten+activation@bx.psu.edu

blacklist_file: config/disposable_email_blacklist.conf
registration_warning_message: Please only register one account

user_activation_on: False
activation_grace_period: 6
```

---

### Galaxy Tours

Have their own [tutorial](/training-material/topics/dev//tutorials/interactive-tours/slides.html#1).

---

### Galaxy Webhooks

Have their own [slides](/training-material/topics/dev//tutorials/webhooks/slides.html#1) and [tutorial](/training-material/topics/dev//tutorials/webhooks/tutorial.html).

And also a [documentation](https://docs.galaxyproject.org/en/master/admin/special_topics/webhooks.html)

---

### Adjusting styles

We use SCSS to build our CSS. Among other features it allows defining [variables](https://github.com/galaxyproject/galaxy/blob/release_19.01/client/galaxy/style/scss/theme/blue.scss).

```diff
--- a/client/galaxy/style/scss/theme/blue.scss
+++ b/client/galaxy/style/scss/theme/blue.scss
@@ -2,7 +2,7 @@
-@base-color-1: #2c3143;
+@base-color-1: blue;
 ```

![blue base color](../../images/blue_base.png)

---

## Dynamic Welcome Page

* Customizing the welcome page is quite easy, just edit `$GALAXY_ROOT/static/welcome.html`

* Embedding [twitter feeds](https://publish.twitter.com) is popular, e.g. [usegalaxy.org](https://usegalaxy.org)

* IFrame to embed a blog hosted on the same domain
```html

<h3>News</h3>

<div id="test-rss">
</div>

<script src="https://fqdn/galaxy/static/scripts/libs/jquery/jquery.js">
</script>

<script type="text/javascript">
	$('#test-rss').load('https://fqdn/category/dev/ #content');
</script>
```

---

## Toolbox filtering

```
# -- ToolBox filtering

# Modules from lib/galaxy/tools/toolbox/filters/ can be specified in
# the following lines.  tool_* filters will be applied for all users
# and can not be changed by them.  user_tool_* filters will be shown
# under user preferences and can be toggled on and off at
# runtime.  Example shown below are not real defaults (no custom
# filters are applied by default), but can be enabled by renaming the
# examples.py.sample in the filters directory to examples.py.

#tool_filters =
#tool_label_filters =
#tool_section_filters =
#user_tool_filters: examples:restrict_upload_to_admins, examples:restrict_encode
#user_tool_section_filters: examples:restrict_text
#user_tool_label_filters: examples:restrict_upload_to_admins, examples:restrict_encode

# The base modules that are searched for modules as described above
# can be modified and modules external to Galaxy can be searched by
# modifying the following option.
#toolbox_filter_base_modules: galaxy.tools.toolbox.filters,galaxy.tools.filters
```

---

## Quotas

Used to control user disk usage.

To turn on the use of quotas: In `galaxy.yml`:
* `enable_quotas` Enable enforcement of quotas.  Quotas can be set from the Admin interface (under Data).
* must create quotas in admin interface before any quota will be enforced, otherwise 'unlimited'

Amounts:
 - Examples: "10000MB", "99 gb", "0.2T", "unlimited"
 - = / + / -

Default for user class:
 - None (No)
 - Unregistered Users
 - Registered Users

or associated with Groups or Users

---

## Exercise: Creating Quotas

* Create quotas for Unregistered (1b) and Registered Users (1mb)
* Create a quota that adds 1GB
* Create a quota that decreases by 1GB
* Create a quota that grants unlimited

---

## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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		<td><abbr title="These people wrote the bulk of the tutorial, they may have done the analysis, built the workflow, and wrote the text themselves.">Author(s)</abbr></td>
		<td>
			
  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
    Björn Grüning</a>
  
  <a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
    Helena Rasche</a>
  
  <a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-martenson"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" />
    Martin Čech</a>
  
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  <a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo">
    <img src="https://avatars.githubusercontent.com/natefoo?s=36" alt="Nate Coraor avatar" width="36" class="avatar" />
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    <img src="https://avatars.githubusercontent.com/nsoranzo?s=36" alt="Nicola Soranzo avatar" width="36" class="avatar" />
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    <img src="https://avatars.githubusercontent.com/hexylena?s=36" alt="Helena Rasche avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/martenson/" class="contributor-badge contributor-martenson">
    <img src="https://avatars.githubusercontent.com/martenson?s=36" alt="Martin Čech avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann">
    <img src="https://avatars.githubusercontent.com/shiltemann?s=36" alt="Saskia Hiltemann avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening">
    <img src="https://avatars.githubusercontent.com/bgruening?s=36" alt="Björn Grüning avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/TKlingstrom/" class="contributor-badge contributor-TKlingstrom">
    <img src="https://avatars.githubusercontent.com/TKlingstrom?s=36" alt="Tomas Klingström avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70">
    <img src="https://avatars.githubusercontent.com/slugger70?s=36" alt="Simon Gladman avatar" width="36" class="avatar" />
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    <img src="https://avatars.githubusercontent.com/willdurand?s=36" alt="William Durand avatar" width="36" class="avatar" />
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    <img src="https://avatars.githubusercontent.com/bebatut?s=36" alt="Bérénice Batut avatar" width="36" class="avatar" />
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  <a href="/training-material/hall-of-fame/mblue9/" class="contributor-badge contributor-mblue9">
    <img src="https://avatars.githubusercontent.com/mblue9?s=36" alt="Maria Doyle avatar" width="36" class="avatar" />
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Tutorial Content is licensed under <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.<br/>