Galaxy iBridges download is a Galaxy tool that facilitates downloading of objects (files) and collections (folders) from iRODS, and can be integrated in a Galaxy workflow.
Galaxy iBridges upload is a Galaxy tool that facilitates uploading of objects and collections to iRODS, and can be integrated in a Galaxy workflow.
Galaxy iBridges browser is an interactive Galaxy tool that makes it possible to browse through an iRODS instance to locate objects and collections, and select them for use in a Galaxy workflow.
The tools are named for iBridges, the client used for interaction with iRODS.
iBridges download takes an iRODS-path to either a dataobject (file) or collection (directory) as source, and a local path to a directory to download the file or files to as. The module has a variable 'data_dir' as output, pointing to the directory files were downloaded to.
iBridges upload takes a local path to a directory or file as source, and an iRODS-path to either a collection (directory) as target. The module requires an input called 'local_path', pointing to the path to upload.
iBridges browser launches as a Galaxy Interactive Tool that allows the user to browse the objects and collections in the iRODS instance through a web interface.
When running an interactive tool, the interactive tool-icon (three gears) will appear in the Galaxy main menu, to the right of User. Clicking the icon opens a screen listing the interactive tools that are running. This can also be reached using the option Active Interactive Tools in the User-item of the main menu. If the icon and the option in the User-menu aren't there, it means no interactive tools are running. If they appear briefly and then disappear, launching of the tool was unsuccesful.
Next, open the tool by clicking 'ibridges browser' in the Active Interactive Tools-list (if the link isn't clickable, the tool is still starting). A new tab will open with a simple web page listing the dataobjects and collections in the user's home folder for the iRODS instance. Navigate through the instance by clicking collections' names, and the links in the breadcrumb path.
To select a path as output for the module, navigate to the appropriate collection and click the 'select'-button. The interactive tool will terminate, signalling to Galaxy that exectution of the workflow can continue. The selected path will be available as the module output parameter 'iRODS path' (this will take a few seconds). Alternatively, you can also copy the path without quitting to your computer's clipboard by clicking 'copy'. To quit without selecting a path, click 'quit' or close the page; the value of the 'iRODS path' parameter will be None.
Please note that the tools' web page cannot close itself; close it by hand once you're done.
The three tools are available in the Galaxy Toolshed as a single module called 'ibridges', and can be installed via the Toolshed (Toolshed link).
Currenly the tools can work with only one iRODS instance per installation.
Add the following to config/user_preferences_extra_conf.yml (create the file if it doesn't exist):
preferences:
irods_config:
description: Your iRODS account
inputs:
- name: username
label: Username
type: text
required: True
- name: password
label: Data Access Password
type: secret
required: True
- name: env
label: Config
required: True
type: textThis will create a section Your iRODS account with inputs for Username, Data Access Password, and Config in the Galaxy user profile, in which users can store their credentials for accessing the appropriate iRODS instance.
Add the tools to an appropriate section in the config/tool_conf.xml:
<tool file="ibridges/ibridges_download.xml" />
<tool file="ibridges/ibridges_upload.xml" />
<tool file="ibridges/ibridges_browse.xml" />Please note: if you don't need the browse function, omit the third line shown above, and skip the changes to config/galaxy.yml and config/job.yml detailed below.
The browse tool is an interactive tool (essentially a webserver communicating with the iRODS server, running in a Docker container). To enable the running of interactive tools, make sure the following settings are present in the galaxy and gravity sections of config/galaxy.yml (change my_galaxy_domain.com to the domain of the actual Galaxy server):
galaxy:
interactivetools_enable: true
outputs_to_working_directory: true
galaxy_infrastructure_url: http://my_galaxy_domain.com:8080
interactivetools_map: database/interactivetools_map.sqlite
interactivetools_upstream_proxy: false
interactivetools_proxy_host: localhost:4002
gravity:
gx_it_proxy:
enable: true
port: 4002For the running of interactive jobs, add the following to the config/job.yml file (create the file if it doesn't exist):
runners:
local:
load: galaxy.jobs.runners.local:LocalJobRunner
workers: 4
execution:
default: docker_dispatch
environments:
local:
runner: local
docker_local:
runner: local
docker_enabled: true
docker_set_user:
docker_dispatch:
runner: dynamic
type: docker_dispatch
docker_destination_id: docker_local
default_destination_id: localCopy the appropriate server configuration from the section Step 2. Configuring iCommands of the page 'Using iCommands for large datasets', and paste it as a string into the Config input for Your iRODS account (via main Galaxy menu: User > Preferences; link Manage Information). You can leave the iRODS username [email protected] as it is.
Make sure users using the tools have access to the iRODS instance specified in the iRODS environment Users must save their username (e-mail address) and Data Access Password in the appropriate inputs for Your iRODS account. Every time one of the tools needs to access iRODS, it automatically reads the credentials from the user's personal profile, and uses them to log in. Be aware that Data Access Passwords usually have a limited lifespan.
Galaxy iBridges browse uses a Docker container which runs in Galaxy's own Docker-environment. It can be pulled from Utrecht University's package registry, and is pulled automatically by Galaxy, from the specification in ibridges_browse.xml:
[...]
<requirements>
<container type="docker">ghcr.io/utrechtuniversity/ibridges_browse:0.1</container>
</requirements>
[...]If for some reason you want to build your own version of the container, the Dockerfile is available in the docker-src folder of this repo. Make sure to change the value in the 'container' element in ibridges_browse.xml to the appropriate value.
This project is licensed under the terms of the MIT License.