# Apollo not responding? **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** gtn-tutorial\ **Created:** [November 1, 2023, 3:31am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076 "2023-11-01T03:31:16Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 1, 2023, 3:31am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/1 "2023-11-01T03:31:16Z")
Hello, I am working through the tutorial " Refining Genome Annotations with Apollo (prokaryotes)", but the **Create or Update Organism** step fails: ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/cfedb5ec352d0c26071a8424834efacfc8e4eed9.png) Here is the error message: INFO:root:curl [https://usegalaxy.eu/apollo\_api/user/loadUsers](https://usegalaxy.eu/apollo_api/user/loadUsers) -H ‘Content-Type: application/json’ -d ‘{“userId”: “[bburnes01@gmail.com](mailto:bburnes01@gmail.com)”, “username”: “XXXXXXXXX”, “password”: “XXXXXXXXX”}’ INFO: **main** :Determining if add or update required INFO:root:curl Any help is appreciated. Thanks. ---
**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:** [November 1, 2023, 4:32pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/2 "2023-11-01T16:32:04Z")
Hi @brianburnes Would you please post back the link to the exact tutorial you are following? I’ll try to replicate the error, then we can report to the EU admins. Thanks! ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 1, 2023, 5:05pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/3 "2023-11-01T17:05:40Z")
Hi Jenna, Thank you for responding. I have tried to open a JBrowse in Apollo as part of several tutorials: > **[Galaxy Training: New Tutorial: Genome Annotation with Apollo](https://training.galaxyproject.org/training-material/short/N00016)** > > Collection of tutorials developed and maintained by the w... > **[Galaxy Training: Refining Genome Annotations with Apollo](https://training.galaxyproject.org/training-material/short/S00066)** > > Genome annotation is a multi-level process that includes ... > **[Galaxy Training: Refining Genome Annotations with Apollo (prokaryotes)](https://training.galaxyproject.org/training-material/short/T00169)** > > Genome annotation is a multi-level process that includes ... > **[Galaxy Training: Refining Genome Annotations with Apollo (eukaryotes)](https://training.galaxyproject.org/training-material/short/T00170)** > > Genome annotation is a multi-level process that includes ... They all have this step: ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/0/02ce1fe7ea54a867a4397a5426cadcc332afb230.png) But it gives an error message. I tried going directly to Apollo with this link: [https://usegalaxy.eu/apollo](https://usegalaxy.eu/apollo), but it gives this error message: ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/f/f2219e59a1ac3762699fb9b7273f4995868db2c4.png) I have tried to generate a json for Apollo instead of specifying a genome, but I don’t know how. Here is my history, if it helps: > **[Galaxy | Europe](https://usegalaxy.eu/published/history?id=9ac82a45f6d2190c)** > > Galaxy is a community-driven web-based analysis platform for life science research. Thank you so much! Brian ---
**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:** [November 1, 2023, 7:49pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/4 "2023-11-01T19:49:01Z")
Thanks for sharing that. I actually don’t know if this is limited to certain accounts or not. (I was also excluded!) Let’s ask the server admins if they recognized what is going on. ping @bjoern.gruening or maybe @wm75 could you help? Update: Decided to cross post over the EU chat. You can reach that at the bottom of the server’s homepage, or by using the link here [You're invited to talk on Matrix](https://matrix.to/#/!pTWTMgjwPzvoMkeBrf:gitter.im/$lRP3wgQq177UZCnM_HlP1yBL8RwzgFk_C-p-AyJTkdE?via=gitter.im&via=matrix.org&via=matrix.clareira.net) Please keep in mind time differences while waiting for a reply … ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 2, 2023, 2:55am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/5 "2023-11-02T02:55:05Z")
Thanks so much! ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 2, 2023, 8:53am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/6 "2023-11-02T08:53:47Z")
@jennaj neither Björn nor Wolfgang maintain the EU Apollo instance, I’m still maintaining it so please feel free to ping me on such issues. @brianburnes I’ll have time to look at it Friday, and I’ll let you know then! ---
**Author:** ![jdom](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jdom/32/4460_2.png) [@jdom](https://help.galaxyproject.org/u/jdom)\ **Post date:** [November 2, 2023, 9:11am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/7 "2023-11-02T09:11:16Z")
@brianburnes Just a note. The error message from your first post is truncated, most likely because got it from the history entry. ![grafik](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/b/bae991dedc216d78945f6c6492e358813fc8e2f0.png) If you click the ![grafik](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/965a1720171e89cdf450da37127a03ccdb5d0a84.png) icon, you will have access to the complete error message. ![grafik](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/736a257261b49daaf49eee389bdad358475486c3.png) Unsurprisingly, it matches what you get when you visit Apollo directly. I hope that helps when the next issue arises. ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 2, 2023, 7:16pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/8 "2023-11-02T19:16:58Z")
@jdom Thank you, that helps. It says to get permission or choose a different name for organism. I will try another name. ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 3, 2023, 9:53am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/9 "2023-11-03T09:53:37Z")
this is still an unexpected error, since the organism names are allocated per-user (hence the `(gx####)` portion in the organism name. That said, please let us know if that fixes it. ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 3, 2023, 9:59am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/10 "2023-11-03T09:59:32Z")
I’m seeing a _lot_ of organisms in the database without proper identifiers, I wonder what’s wrong there. based on the current deployment of EU, it’s supposed to be included (`GALAXY_APOLLO_ORG_SUFFIX=id"`) ```auto group_vars/all.yml 151:# Apollo env vars 152:apollo_env: "GALAXY_WEBAPOLLO_URL={{ GALAXY_WEBAPOLLO_URL }} GALAXY_WEBAPOLLO_USER={{ GALAXY_WEBAPOLLO_USER }} GALAXY_WEBAPOLLO_PASSWORD={{ GALAXY_WEBAPOLLO_PASSWORD }} GALAXY_WEBAPOLLO_EXT_URL={{ GALAXY_WEBAPOLLO_EXT_URL }} GALAXY_SHARED_DIR={{ GALAXY_SHARED_DIR }} GALAXY_APOLLO_ORG_SUFFIX=id" ``` so, that’s rather unexpected and can be exacerbating this issue; anyone using a common name will encounter these permission errors. @jdom maybe you have some ideas? is this related to the TPV migration somehow, that the env vars aren’t getting passed properly? ---
**Author:** ![jdom](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jdom/32/4460_2.png) [@jdom](https://help.galaxyproject.org/u/jdom)\ **Post date:** [November 3, 2023, 1:51pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/11 "2023-11-03T13:51:12Z")
I debugged [create\_or\_update\_organism.py](https://github.com/galaxy-genome-annotation/galaxy-tools/blob/3407a4e6a60ff89a0ab5eab87ab94b0d9a209500/tools/apollo/create_or_update_organism.py#L134) for a while and so far I found the following. Line 134 sets `org = {'annotationCount': 0, 'blatdb': None, 'commonName': 'E. coli K12 (gx*****)', 'currentOrganism': False, 'directory': '/data/dnb01/apollo/*********', 'genomeFasta': 'seq/genome.fasta', 'genomeFastaIndex': 'seq/genome.fasta.fai', 'genus': 'Escherichia', 'id': *******, 'metadata': '{"creator":"**"}', 'nonDefaultTranslationTable': None, 'obsolete': False, 'publicMode': False, 'sequences': 2, 'species': 'coli', 'valid': True}`. Execution continues until [line 148](https://github.com/galaxy-genome-annotation/galaxy-tools/blob/3407a4e6a60ff89a0ab5eab87ab94b0d9a209500/tools/apollo/create_or_update_organism.py#L148). In [accessible\_organisms](https://github.com/galaxy-genome-annotation/python-apollo/blob/1257e050ee3fc0a7f7ab8a8c780aefee5c8143f8/apollo/ __init__.py#L67-L75), both `permission_map` (a dict) and `user.organismPermissions` are empty. Thus, an empty list is returned, triggering the exception on [line 150](https://github.com/galaxy-genome-annotation/galaxy-tools/blob/3407a4e6a60ff89a0ab5eab87ab94b0d9a209500/tools/apollo/create_or_update_organism.py#L150). The `user` passed to `accessible_organisms` is created [here](https://github.com/galaxy-genome-annotation/galaxy-tools/blob/3407a4e6a60ff89a0ab5eab87ab94b0d9a209500/tools/apollo/create_or_update_organism.py#L118). The content of `wa.users._assert_or_create_user(args.email)` is ```auto {'firstName': 'Brian ', 'lastName': 'Burnes', 'inactive': False, 'role': 'USER', 'availableGroups': [ {'name': ' ****'}, ..., {'name': ' ****'}, {'name': ' ****'}, {'name': ' ****'}], 'userCount': 1, 'searchName': None, 'groups': [], 'userId': ******* , 'organismPermissions': [], 'username': 'bburnes01@gmail.com'} ``` The value for the key `organismPermissions` is an empty list. Digging deeper, that information [comes from the `loadUsers` endpoint](https://github.com/galaxy-genome-annotation/python-apollo/blob/1257e050ee3fc0a7f7ab8a8c780aefee5c8143f8/apollo/users/ __init__.py#L84). Feel free to continue debugging if you find some time for it. ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 13, 2023, 5:24pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/12 "2023-11-13T17:24:22Z")
Hi JDOM, @jdom I am still trying to use this tool. When I try to call up Apollo, I am getting this error: (What does “list index out of range” mean? ```auto "/opt/galaxy/shed_tools/[toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/9e7b8c7185ad/apollo_create_or_update/create_or_update_organism.py](http://toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/9e7b8c7185ad/apollo_create_or_update/create_or_update_organism.py)", line 123, in org_cn = org_cn[0] IndexError: list index out of range ``` ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 15, 2023, 5:25pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/13 "2023-11-15T17:25:55Z")
Hi Helena, @hexylena I am still trying to use this tool. When I try to use Apollo, I am getting this “list index out of range” error. Any ideas? Thanks. ```auto "/opt/galaxy/shed_tools/[toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/9e7b8c7185ad/apollo_create_or_update/create_or_update_organism.py](http://toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/9e7b8c7185ad/apollo_create_or_update/create_or_update_organism.py)", line 123, in org_cn = org_cn[0] IndexError: list index out of range ``` ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 16, 2023, 8:38am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/14 "2023-11-16T08:38:11Z")
@jdom did you check if the env var `galaxy_apollo_org_suffix` was properly set? ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 24, 2023, 1:38pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/15 "2023-11-24T13:38:47Z")
Ok, I can confirm some issue in creating the organism, it’s created on the backend without assigning permissions properly. I’m investigating currently. ---
**Author:** ![hexylena](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/hexylena/32/4171_2.png) [@hexylena](https://help.galaxyproject.org/u/hexylena)\ **Post date:** [November 24, 2023, 1:57pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/16 "2023-11-24T13:57:20Z")
Ok, here’s how the bug happens: - Galaxy EU launches a job - It runs on a cluster somewhere - **A** This job contacts [https://usegalaxy.eu/apollo\_api/](https://usegalaxy.eu/apollo_api/) - **B** That server passes the request to [https://apollo.internal/apollo\_api/](https://apollo.internal/apollo_api/) - Which passes it on to [http://localhost:8080/apollo/](http://localhost:8080/apollo/) - The creation script crashes - And never reaches the step to add permissions for your user to access the organism. This request takes more than 60 seconds, which means proxy B says the request timed out, and proxy A also fails it, which ends up back in the job. We (@abretaud) and I proxy the request to `/organism/findAllOrganisms` through a project [GitHub - galaxy-genome-annotation/apolpi: Partial, faster reimplementation of Apollo API](https://github.com/galaxy-genome-annotation/apolpi) because of how slow it is, to avoid this issue in other situations. However, creating an organism _also_ generates this same list of organisms, a process that currently takes 74 seconds on EU. We can bump the timeouts as a short term solution which should help, but long term, hopefully this can be fixed by Apollo3. I’ve requested an infrastructure change at EU, hopefully they can merge it soon 🙂 [Increase proxy timeout for apollo by hexylena · Pull Request #1013 · usegalaxy-eu/infrastructure-playbook · GitHub](https://github.com/usegalaxy-eu/infrastructure-playbook/pull/1013) ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [November 25, 2023, 10:59pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/17 "2023-11-25T22:59:21Z")
Thank you, Helena! ---
**Author:** ![jdom](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jdom/32/4460_2.png) [@jdom](https://help.galaxyproject.org/u/jdom)\ **Post date:** [December 6, 2023, 2:58pm UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/18 "2023-12-06T14:58:50Z")
@brianburnes Is Apollo now working or do you still have issues? ---
**Author:** ![brianburnes](https://avatars.discourse-cdn.com/v4/letter/b/ac91a4/32.png) [@brianburnes](https://help.galaxyproject.org/u/brianburnes)\ **Post date:** [December 8, 2023, 1:27am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/19 "2023-12-08T01:27:26Z")
YES, it worked!!! So, I was checking an existing history and rerunning the “Create or update organism” tool, but it kept failing. Then, I rebuilt the history and it ran just fine. Thank you so much for your help. Hooray, Galaxy!!! ---
**Author:** ![jdom](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jdom/32/4460_2.png) [@jdom](https://help.galaxyproject.org/u/jdom)\ **Post date:** [December 8, 2023, 11:22am UTC](https://help.galaxyproject.org/t/apollo-not-responding/11076/20 "2023-12-08T11:22:23Z")
Awesome! @jennaj I assume only @brianburnes or a forum admin can mark this as solved right? [Next page](https://help.galaxyproject.org/t/apollo-not-responding/11076.md?page=2)