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Gearing towards production

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last_modification Published: Jan 28, 2019
last_modification Last Updated: Apr 16, 2023

Production server

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Configuration Options

Speaker Notes


class: reduce90

Configuring uWSGI

Important options in the uwsgi section of galaxy.yml

option description
http port and IP on which to listen for HTTP requests, :8080 for port 8080 on all network interfaces. For a production server, you should use socket: and a proxy server.
socket port and IP on which to listen for uWSGI protocol requests, 127.0.0.1:8000 for port 8000 on localhost.
processes number of uWSGI web workers.
threads number of threads for each web worker.
offload-threads number of threads for internal routing requests, 1-2 is sufficient.
master use uWSGI master process manager, defaults to false for dev compatibility but should be true in production.
mule-reload-mercy time to gracefully wait for mule shutdown, set > monitor_thread_join_timeout galaxy option.

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Securing your Object IDs

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Customizing your “Brand”

option description
brand appends “/{brand}” to the “Galaxy” text in the masthead.
logo_url URL linked by the “Galaxy/brand” text.
helpsite_url URL linked by the “Galaxy Help” link in the “Help” menu.
wiki_url URL linked by the “Wiki” link in the “Help” menu.
support_url URL linked by the “Support” link in the “Help” menu.
citation_url URL linked by the “How to Cite Galaxy” link in the “Help” menu.
search_url URL linked by the “Search” link in the “Help” menu.
mailing_lists_url URL linked by the “Mailing Lists” link in the “Help” menu.
screencasts_url URL linked by the “Videos” link in the “Help” menu.
terms_url URL linked by the “Terms and Conditions” link on the registration form.
qa_url URL linked by the “Galaxy Q&A” link in the “Help” menu.

Speaker Notes


Adding a Notice Banner

option sample value
message_box_visible true
message_box_content Downtime scheduled Sunday at Noon to one.
message_box_class warning (also: error, info)

Speaker Notes


Update the welcome page

Welcome page is $GALAXY_ROOT/static/welcome.html and is the first thing that users see. It is a good idea to extend it with things like:

.left[No restarting is necessary.]

Speaker Notes


Client Browser Security

option description
sanitize_all_html by default, Galaxy sanitizes all “text/html” tool outputs. Setting to false potentially exposes users to XSS attacks.
sanitize_whitelist_file manually override html sanitization for listed tools. Can set in admin interface.
serve_xss_vulnerable_mimetypes certain filetypes (e.g. SVG) can contain JS that is vulnerable to XSS (Cross-site scripting) and are served as “plain/text” by default.
allowed_origin_hostnames Returns Access-Control-Allow-Origin response header that matches the Origin header of the request.

Speaker Notes


Debugging

These should never be enabled on a public site.

option description
debug enable debug options, preserves cluster job data on disk (but use cleanup_job for this).
use_profile Python profiler on requests.
use_printdebug Anything “print”ed within a Galaxy Web thread is exposed to user.
use_interactive Enable live debugging in your browser.

Speaker Notes


Configuring FTP

option description
ftp_upload_dir Directory containing subdirectories matching users’ identifier (defaults to e-mail).
ftp_upload_site Hostname of your FTP server provided to users in the help text. Must set to enable FTP import.
ftp_upload_dir_identifier User attribute for subdirectory naming. ‘email’ (${user.email}) is default, but ‘id’ or ‘username’ are also common.
ftp_upload_dir_template Python string template used to determine a users FTP upload directory (${ftp_upload_dir}/${ftp_upload_dir_identifier}).
ftp_upload_purge Delete files after FTP import (true).

Speaker Notes


class: reduce90

Configuring Data Library Path Uploads

Admin options

option description
library_import_dir Browse and upload files from configured directory.
allow_path_paste Allow admins to paste any path to upload (e.g. file://), applies also to the general ‘upload tool’.

User options

option description
user_library_import_dir Root directory containing sub-directories named by user emails. A nifty setup is that the value is the same as for ftp_upload_dir allowing users to upload files via FTP and then import them either in history or data library.
user_library_import_dir_auto_creation Create user’s folder upon login.
user_library_import_symlink_whitelist Directories that users are allowed to symlink to.
user_library_import_check_permissions If Galaxy usernames match system usernames enable this to use UNIX permissions.

Speaker Notes


class: reduce90

Configuring SMTP

SMTP server

option description
smtp_server host:port of SMTP server to use. Uses STARTTLS, but will fallback.
smtp_username Username for SMTP server.
smtp_password Password for SMTP server. STARTTLS recommended on SMTP server.
smtp_ssl If SMTP server requires SSL from connection start, set to true.

Addresses

option description
error_email_to Address to send user error reports to.
email_from Return address used in automatic user notifications. (<galaxy-no-reply@HOSTNAME>)
mailing_join_addr Mailing list to subscribe users to during registration.

Speaker Notes


galaxy.yml full options

a.k.a. Everything You Always Wanted to Know About galaxy.yml

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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.