Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bring your own file source: Add webdav template and update ansible conf #1279

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
44 changes: 44 additions & 0 deletions files/galaxy/config/file_source_templates/production_webdav.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
- id: webdav
version: 0
name: WebDAV
description: |
The WebDAV protocol is a simple way to access files over the internet. This template
configuration allows you to connect to a WebDAV server.
variables:
url:
label: Server Domain (e.g. https://myowncloud.org)
type: string
help: |
The domain of the WebDAV server you are connecting to. This should be the full URL
including the protocol (http or https) and the domain name.
root:
label: WebDAV server Path (should end with /remote.php/webdav, e.g. /a/sub/path/remote.php/webdav)
type: string
help: |
The full server path to the WebDAV service. Ensure the path includes /remote.php/webdav.
login:
label: Username
type: string
help: |
The username to use to connect to the WebDAV server. This should be the username you use
to log in to the WebDAV server.
writable:
label: Writable?
type: boolean
default: false
help: Allow Galaxy to write data to this WebDAV server.
secrets:
password:
label: Password
help: |
The password to use to connect to the WebDAV server. This should be the password you use
to log in to the WebDAV server.
configuration:
type: webdav
url: '{{ variables.url }}'
root: '{{ variables.root }}'
login: '{{ variables.login }}'
writable: '{{ variables.writable }}'
password: '{{ secrets.password }}'
use_temp_files: true
temp_path: /data/jwd04/tmp
4 changes: 4 additions & 0 deletions group_vars/sn06.yml
Original file line number Diff line number Diff line change
Expand Up @@ -292,6 +292,7 @@ galaxy_server_dir: "{{ galaxy_root }}/server"
galaxy_config_dir: "{{ galaxy_root }}/config"
galaxy_venv_dir: "{{ galaxy_root }}/venv"
galaxy_job_working_directory: "{{ galaxy_config['galaxy']['job_working_directory'] }}"
galaxy_file_source_templates_dir: "{{ galaxy_mutable_config_dir }}/file_source_templates"
ucsc_build_sites:

galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv --copies"
Expand All @@ -318,6 +319,7 @@ galaxy_dirs:
- "{{ galaxy_log_dir }}"
- "{{ galaxy_config_dir }}/total_perspective_vortex"
- "{{ tpv_mutable_dir }}"
- "{{ galaxy_file_source_templates_dir }}"

galaxy_instance_hostname: usegalaxy.eu
galaxy_config_style: yaml
Expand Down Expand Up @@ -422,6 +424,8 @@ galaxy_config_files:
dest: "{{ tpv_mutable_dir }}/interactive_tools.yml"
- src: "{{ galaxy_config_file_src_dir }}/tpv/users.yml"
dest: "{{ tpv_mutable_dir }}/users.yml"
- src: "{{ galaxy_config_file_src_dir }}/config/file_source_templates/production_webdav.yml"
dest: "{{ galaxy_file_source_templates_dir }}/production_webdav.yml"

#- src: files/galaxy/config/job_resource_params_conf.xml
#dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}"
Expand Down
3 changes: 3 additions & 0 deletions templates/galaxy/config/file_source_templates.yml.j2
Original file line number Diff line number Diff line change
Expand Up @@ -4,3 +4,6 @@
- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_s3fs.yml"
- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml"
- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml"

# These templates are maintained by EU
- include: "{{ galaxy_file_source_templates_dir }}/production_webdav.yml"
Loading