Welcome @SaibotMagd
I’m not sure which server you are working at (the URL) but if that target server supports an OMERO connections, this is how to access your user preferences at a Galaxy server.
Create or log into your account.
This is a simple guide that will apply to most Galaxy servers → FAQ: How do I create an account on a public Galaxy instance?. The screenshots are for a different release, but maybe comparing to the new screenshots I’m including here will help to get your oriented too, no matter which release may be running?
Click into the User menu in the masthead (to the right at the top)
The preferences will list out the options available at that server.
The Manage Information section is where most of the external keys and configurations are set up but you can explore the others. Some common examples are in this guide → FAQ: How to update account preferences?
One server that supports the OMERO connection is UseGalaxy.eu.
Please let us know if this actually helps or not! Maybe share a screenshot of where you are stuck that includes the server URL at top. We can help to double check if this option is supported or not there, and maybe look into why.
And I just re-read – is this really on a local server? What does your deployment looks like? Have you tried the instructions here yet? tools-iuc/tools/idr_download/README.md at main · galaxyproject/tools-iuc · GitHub (linked at the bottom of the blog post). I wasn’t sure if you just had trouble finding it or if the config is the issue. The version of Galaxy would be helpful and please note if the Docker Galaxy or something different we can point you to the correct administration docs for locating config files. Xref → Private Galaxy Servers
Thanks! 
Yes its a local server installed from by using the Docker image: GitHub - bgruening/docker-galaxy: 🐋📊📚 Docker Images tracking the stable Galaxy releases. I’m in contact with Björn Gröning but we couldn’t find a solution yet. The credential menu just doesn’t apear in the preferences menu not for omero nor ownloud or anything else. its just empty as it is. I used every guide you posted and tried on every file. So the issue seems somewhere else.
Since I have identified and resolved all the issues that arose from my perspective and the connection is functioning, the galaxy topic is now closed for me. The issues and limitations are simply too significant to warrant further pursuit. However, it may be possible to revisit this at a later stage once the project has progressed sufficiently. However, I cannot invest any more resources and am looking for another solution. Here is the documentation of what I have found out. PS: These are my own findings and conclusions that I have drawn from them. I cannot validate them or uncover the causes. In other words, everything could be completely wrong:
- The goal was to link the Docker installation of OMERO (\https://github.com/ome/docker-example-omero) with that of Galaxy-Project (\https://github.com/bgruening/docker-galaxy).
- The end result should be installation instructions that are as easy to follow as possible for installing the entire package consisting of OMERO, OMERO-web, OMERO.insight, Galaxy Project (including shed-tools, interactiven and jupyter-lite) locally in the shortest possible time, preferably completely container-based for better scalability.
- The OMERO Docker installation ran as described in the documentation.
- The galaxy-project installation initially had important restrictions in that the services curl, requests (python package) and mercurial require an somewhat unrestricted internet connection; i.e. since we use SSL-inspection in our company, the local certificate must be transferred to all services, as well as to the locally running docker service. This works as follows, for example:
docker run -p 8080:80 -p 8021:21 -p 4002:4002
–network=galaxy-omero
–privileged=true
-v /galaxy-vol/:/export/
-v /var/run/docker.sock:/var/run/docker.sock
-v /galaxy-docker/hgrc:/etc/mercurial/hgrc:ro
-v /etc/ssl/certs/ca-certificates.crt:/etc/ssl/certs/ca-certificates.crt:ro
-e SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt
-e REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
-e CAFILE=/etc/ssl/certs/ca-certificates.crt
-e GALAXY_CONFIG_USER_PREFERENCES_EXTRA_CONF_PATH=/export/galaxy/config/user_preferences_extra_conf.yml
quay.io/bgruening/galaxy
The hgrc file for Mercurial's certificate path looks like this:
[web]
cacerts = /etc/ssl/certs/ca-certificates.crt
- As shown in the command, 4 containers (OMERO postgressql, OMERO.web, OMERO.server, galaxy-docker) must be linked in a bridge
- With
docker inspect {bridgename}
you can find out which IP address the OMERO.server has, as you have to enter this in the galaxy omero plugin (the container name also works)
user_preferences_extra_conf.yml.sample
must be renamed to .yml and you must enter the following data as described in https://github.com/galaxyproject/tools-iuc/blob/main/tools/idr_download/README.md:
omero_account:
description: Your OMERO instance connection credentials
inputs:
- name: username
label: Username
type: text
required: False
- name: password
label: Password
type: password
required: False
# Call the main function to get the object and save it as a TSV
get_ids_ezo(user=crds[‘username’], pws=crds[‘password’], host=args.host,
port=args.port,
final_obj_type=args.final_obj_type,
parent_obj_type=args.parent_obj_type,
parent_id=args.parent_id,
tsv_file=args.tsv_file)
Seems that you are nearly there.
The user has set up the the omero_account credentials?
However, what does not work for me is writing the credentials_file… This is always empty.
Is there an error in the logs? Can you post the content of the log file? What is the content of the credentials file in the job working dir?
I don’t know which log you mean. The one from the container? The one from the respective tool-shed extension? Or the one from Galaxy itself? All three are long and full of errors. I’ll try to find them all. … so I don’t think I’m on a good way or nearly close to succeed. And even if I could make it run, then there’s an even longer way to application.
The credentials file only exists while the respective command of the respective extension is being executed and is always empty.
However, the next answer may take a while, because in my work process I only have a certain amount of time available for each task and then have to stop working on it once that time has elapsed, regardless of its status. In this case, I have already exceeded the time limit by at least 40 hours.
Dear @SaibotMagd.
I mean the log of Galaxy itself. Relevant will be the part from when you trigger the tool run until it is finished.
Also anything vault/omero related that is printed during startup of Galaxy could help as well.
The credentials file only exists while the respective command of the respective extension is being executed and is always empty.
Just to be sure: If you go to the user preferences you can see that the credentials are set?
