# Galaxy 25\_0 on GCE, Microarray Tissue Analysis tutorial, ImageJ installation **URL:** \ **Category:** Uncategorized\ **Tags:** devops-administration, iwc-workflows\ **Created:** [July 8, 2025, 3:23am UTC](https://help.galaxyproject.org/t/galaxy-25-0-on-gce-microarray-tissue-analysis-tutorial-imagej-installation/15922 "2025-07-08T03:23:59Z")\ **Posts on this page:** 1\ **Showing post:** 14
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [July 10, 2025, 7:04pm UTC](https://help.galaxyproject.org/t/galaxy-25-0-on-gce-microarray-tissue-analysis-tutorial-imagej-installation/15922/14 "2025-07-10T19:04:21Z")
> [@GaryAitken](#): > > What do you mean by a fresh checkout? git clone -b release\_25.0 **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](https://docs.galaxyproject.org/en/master/admin/config.html#configuration-basics) **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](https://github.com/bgruening/docker-galaxy/blob/main/README.md) > [@GaryAitken](#): > > When and how is the tool dependency supposed to be resolved? 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. > [@jennaj](#): > > Your other option is the **Docker Galaxy** deployment. This involves some pre-requisite set up with a Docker environment first, but it will be much simpler to install and maintain, and you might find it nicer to work with. That will allow you to use **Ephemeris** scripts like this one to set your server → [Hands-on: End-to-End Tissue Microarray Image Analysis with Galaxy-ME / End-to-End Tissue Microarray Image Analysis with Galaxy-ME / Imaging](https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html#admin-missing-tools) (admin-missing-tools) using this procedure → [Hands-on: Galaxy Tool Management with Ephemeris / Galaxy Tool Management with Ephemeris / Galaxy Server administration](https://training.galaxyproject.org/training-material/topics/admin/tutorials/tool-management/tutorial.html). Be sure to see the Docker Galaxy README since some of this is pre-configured for you, as this version of Galaxy was designed to be used by scientists doing exactly what you are. * * * 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. > [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1): > > Training Network [Galaxy server administration training](https://training.galaxyproject.org/training-material/topics/admin/) * * * **The basic steps are** 1. Create the environment you plan to install Galaxy into 2. Clone Galaxy into that environment 3. Start Galaxy up and resolve any issues reported 4. Set basic configurations about how data is saved, which logs are written, where jobs will run, and related details. 5. 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. 6. 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: > [@GaryAitken](#): > > Don’t know if this helps or not: the basic\_illumination tool is already present in the [usegalaxy.eu](http://usegalaxy.eu) server. It appears to have already been used there, so its dependencies are resolved there. I’m guessing the server was built with the tool and its dependencies already included, as opposed to being dynamically loaded. It might be worth verifying that. Whether or not it has been successfully used I cannot tell; All of the dependencies for a tool are installed by the administrator, before the user is using a tool. > [@GaryAitken](#): > > if I try to run it on the [usegalaxy.eu](http://usegalaxy.eu) server, I get the following error with each image: > > ```auto > Cannot display TIFF image > getUint16@https://usegalaxy.eu/static/plugins/visualizations/tiffviewer/static/index.js:3:21331 > fromSource@https://usegalaxy.eu/static/plugins/visualizations/tiffviewer/static/index.js:5:215 > Reason: offset is outside the bounds of the DataView > > ``` 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](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) and post that back here for troubleshooting. I would also suggest trying to load your test images at [cancer.GalaxyProject.org](http://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. > [@GaryAitken](#): > > BaSiC\_Illumination is not already present in the [usegalaxy.org](http://usegalaxy.org) server. What happens if an admin dynamically loads it (it will load ok) and then tries to execute it? Does it fail because of the inability to find ImageJ, or does it get further along? I found the tool at [UseGalaxy.org](http://UseGalaxy.org). Do I have the right tool here? - **BaSiC Illumination** ImageJ BaSiC shading correction for use with Ashlar ([link at ORG](https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.1.1+galaxy2)) 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. ```auto --- 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..) ``` --- _[View the full topic](https://help.galaxyproject.org/t/galaxy-25-0-on-gce-microarray-tissue-analysis-tutorial-imagej-installation/15922)._