Local Galaxy: Yes, create a new empty default .venv
directory, git clone the release, then start up Galaxy for the first time. At this step, you’ll want to make sure the logs do not report any problems (resolve these), and that you can locate your local server through a browser on your computer. See → Galaxy Configuration — Galaxy Project 25.0.2.dev0 documentation
Docker Galaxy (alternative): follow the instructions here. You will be cloning the docker image into a docker environment instead. docker-galaxy/README.md at main · bgruening/docker-galaxy · GitHub
The tool dependency resolution happens when a tool is installed. A repository from the ToolShed contains all of the details.
Using the resources from the tutorial through the Ephemeris process will access the ToolShed to pull in the tool repositories. Each is resolved during installation. The script batches this all together.
Both options are a full Galaxy server! The configuration for a single-user will be mostly the defaults for both.
If you plan to have multiple users or to connect to a computing cluster, the default options in Docker Galaxy will be easier to configure, and it has the README with the exact instructions. This version was designed to be used by people (scientists, teachers, but also developers) who want one or more quick Galaxy instances up and running.
If you plan to do that with the Local Galaxy, this will be a larger project with many configurations. Following the Admin Training → Learning Pathway here is strongly recommended.
The basic steps are
- Create the environment you plan to install Galaxy into
- Clone Galaxy into that environment
- Start Galaxy up and resolve any issues reported
- Set basic configurations about how data is saved, which logs are written, where jobs will run, and related details.
- Then you can start to customize the tool and data content: installing tools and reference data. This is when all of the dependencies for each tool (including visualization components) are installed.
- Once those are done, you are ready to work in Galaxy in a similar way to how you work at a public Galaxy server.
Does this helps?
Then back to the data test question:
All of the dependencies for a tool are installed by the administrator, before the user is using a tool.
The error is suggesting that there is some data content issue with the TIFF file. My first guess is a coordinate problem between what the display is expecting, and the data provided, likely a file format issue, maybe related to version changes. Maybe there is a way to standardize or otherwise correct the data.
I can help to confirm this, and to report issues to the developers (if needed) but I would need to see the actual data in the history to do this. You are welcome to generate a history share link and post that back here for troubleshooting.
I would also suggest trying to load your test images at cancer.GalaxyProject.org, since that is the server where these spacial omics tool are developed. Problems (or success!) as a comparison would help with any troubleshooting, too.
I found the tool at UseGalaxy.org. Do I have the right tool here?
- BaSiC Illumination ImageJ BaSiC shading correction for use with Ashlar (link at ORG)
This tool would be installed with all dependencies if you use the Ephemeris script. This is what the first lines in the script are configuring. They are telling Galaxy to pull all the dependencies in, in the exact version that the tool needs to function correctly.
---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools:
(..other tools..)
- name: basic_illumination
owner: perssond
revisions: 7ee5b6f7533e
tool_panel_section_label: Spatial Omics
tool_shed_url: https://toolshed.g2.bx.psu.edu/
(..more tools..)