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Advanced customisation of a Galaxy instance

Contributors

Authors: orcid logoBjörn Grüning avatar Björn Grüningorcid logoHelena Rasche avatar Helena Rascheorcid logoMartin Čech avatar Martin Čech
Published: Jun 27, 2017
Last Updated: Apr 17, 2023

Setup

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

From the given USB stick, please:

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:

$ cd $GALAXY_ROOT
$ make client

This requires Node.

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.

_l( 'Help' )

–

"Analyze Data" :
    false,

–

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

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

Tool Panel configuration

Tool panel labels

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

tool panel labels

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.

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

# 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

# Verbosity of console log messages.
log_level: DEBUG

These are python logging levels.

log levels

Help menu

# 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

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

brand

# 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

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.

Galaxy Webhooks

Have their own slides and tutorial.

And also a documentation

Adjusting styles

We use SCSS to build our CSS. Among other features it allows defining variables.

--- 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

Dynamic Welcome Page

–

–

News


---

## 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:

Amounts:

Default for user class:

or associated with Groups or Users

Exercise: Creating Quotas

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! page logo Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.