# \#galaxy-local **URL:** https://help.galaxyproject.org/tag/galaxy-local/58.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [HUMAnN error version](https://help.galaxyproject.org/t/humann-error-version/18284)
**Author:** [@Reki](https://help.galaxyproject.org/u/Reki)\ **Replies:** 1\ **Last updated:** [August 14, 2026, 8:10pm UTC](https://help.galaxyproject.org/t/humann-error-version/18284 "2026-08-14T20:10:44Z")
Galaxy Microbiology HUMAnN 3.9+galaxy1 Error: "The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJun23" The only MetaPhlAn marker database available under “Locally cache… --- ## [Errors during starting Galaxy on local server](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158)
**Author:** [@Charmax](https://help.galaxyproject.org/u/Charmax)\ **Replies:** 3\ **Last updated:** [July 10, 2026, 1:05pm UTC](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158 "2026-07-10T13:05:59Z")
I was trying to run galaxy on a server for around 1 week. However after I cloned the git repository and started “sh run.sh” directly, there were two error messages showing up: galaxy.tool\_util.toolbox.integrated\_panel… --- ## [Long waiting times until metadata is set](https://help.galaxyproject.org/t/long-waiting-times-until-metadata-is-set/17752)
**Author:** [@casio](https://help.galaxyproject.org/u/casio)\ **Replies:** 4\ **Last updated:** [May 27, 2026, 6:03pm UTC](https://help.galaxyproject.org/t/long-waiting-times-until-metadata-is-set/17752 "2026-05-27T18:03:06Z")
Hi everyone, I am reaching out because I have hit a major performance wall with my Galaxy instance and could use some advice from the community. I am currently managing a 160 TB instance where the entire database and d… --- ## [Hosting to UCSC with Custom Builds](https://help.galaxyproject.org/t/hosting-to-ucsc-with-custom-builds/17676)
**Author:** [@GalaxyFrog](https://help.galaxyproject.org/u/GalaxyFrog)\ **Replies:** 5\ **Last updated:** [April 25, 2026, 4:21pm UTC](https://help.galaxyproject.org/t/hosting-to-ucsc-with-custom-builds/17676 "2026-04-25T16:21:51Z")
I love Galaxy! I’m working with the white-tail deer genome build, which is curated by UCSC in it’s most recent form as Ovbor\_1.2 Oct. 2024 white-tailed deer (Illinois 20LAN1187 2024) (GCF\_023699985.2). As near as I can … --- ## [Accessiblity statement or VPAT for compliance](https://help.galaxyproject.org/t/accessiblity-statement-or-vpat-for-compliance/17657)
**Author:** [@psdavis](https://help.galaxyproject.org/u/psdavis)\ **Replies:** 1\ **Last updated:** [April 17, 2026, 7:03pm UTC](https://help.galaxyproject.org/t/accessiblity-statement-or-vpat-for-compliance/17657 "2026-04-17T19:03:48Z")
Hey All, I administer a local galaxy install on a small computational cluster at a tier 2 institution in the United States. I’m looking for a VPAT or some other formal documentation of accessibility to pas on to our adm… --- ## [Search Data Libraries Datasets](https://help.galaxyproject.org/t/search-data-libraries-datasets/2755)
**Author:** [@Thahmina](https://help.galaxyproject.org/u/Thahmina)\ **Replies:** 1\ **Last updated:** [April 7, 2026, 9:52pm UTC](https://help.galaxyproject.org/t/search-data-libraries-datasets/2755 "2026-04-07T21:52:27Z")
Greetings, I know that searching on data library names and descriptions is possible, but I am trying to find the feature that enables the ability to search on names, descriptions or attributes of data library datasets. … --- ## [Put() not working in jupyter notebook on local server](https://help.galaxyproject.org/t/put-not-working-in-jupyter-notebook-on-local-server/17535)
**Author:** [@rheiland](https://help.galaxyproject.org/u/rheiland)\ **Replies:** 5\ **Last updated:** [March 5, 2026, 10:11pm UTC](https://help.galaxyproject.org/t/put-not-working-in-jupyter-notebook-on-local-server/17535 "2026-03-05T22:11:24Z")
I’ve cloned the latest 26.0 release and trying, but failing, to use put() from a Jupyter notebook on my local server. And apologies, as I think I’ve gone through this previously - if so, my notes fail me. I see there a… --- ## [Failed to find virtualenv when building galaxy from ansible tutorial](https://help.galaxyproject.org/t/failed-to-find-virtualenv-when-building-galaxy-from-ansible-tutorial/17529)
**Author:** [@GaryAitken](https://help.galaxyproject.org/u/GaryAitken)\ **Replies:** 11\ **Last updated:** [March 6, 2026, 11:38pm UTC](https://help.galaxyproject.org/t/failed-to-find-virtualenv-when-building-galaxy-from-ansible-tutorial/17529 "2026-03-06T23:38:42Z")
Trying to install 25.1 on ubuntu 24.04 following ansible install tutorial After 72 tasks (ok=38, skipped=34), it fails looking for executable “virtualenv”: TASK \[galaxyproject.galaxy : Report Galaxy version change\] ski… --- ## [Interactive Tools in a Dockerized Galaxy instance](https://help.galaxyproject.org/t/interactive-tools-in-a-dockerized-galaxy-instance/17453)
**Author:** [@JBoom](https://help.galaxyproject.org/u/JBoom)\ **Replies:** 1\ **Last updated:** [February 12, 2026, 7:50pm UTC](https://help.galaxyproject.org/t/interactive-tools-in-a-dockerized-galaxy-instance/17453 "2026-02-12T19:50:37Z")
Good day everyone! I was hoping someone might be able to help me with some issues around running Interactive Tools inside a Docker‑based Galaxy deployment. Our current setup: We maintain our own Docker image, based l… --- ## [Issue upgrading database for local Galaxy](https://help.galaxyproject.org/t/issue-upgrading-database-for-local-galaxy/17296)
**Author:** [@paige\_kulzer](https://help.galaxyproject.org/u/paige_kulzer)\ **Replies:** 1\ **Last updated:** [January 23, 2026, 11:16pm UTC](https://help.galaxyproject.org/t/issue-upgrading-database-for-local-galaxy/17296 "2026-01-23T23:16:54Z")
Hello! I’m trying to start a local instance of Galaxy following these instructions: Get Galaxy | Galaxy Hub I’ve done this successfully with a past release of Galaxy but this most recent release is giving me trouble. W… --- ## [Galaxy 25.0 ran into javascript heap out of memory error during client installation](https://help.galaxyproject.org/t/galaxy-25-0-ran-into-javascript-heap-out-of-memory-error-during-client-installation/16063)
**Author:** [@mariabernard](https://help.galaxyproject.org/u/mariabernard)\ **Replies:** 3\ **Last updated:** [January 13, 2026, 7:38am UTC](https://help.galaxyproject.org/t/galaxy-25-0-ran-into-javascript-heap-out-of-memory-error-during-client-installation/16063 "2026-01-13T07:38:45Z")
Hi there, I am trying to install the last version of Galaxy (25.0.0) but I encountered an OOM error. This occure during the client installation. Here are the last log lines: Browserslist: caniuse-lite is outdated. Ple… --- ## [Admin in local installation impossible to make work](https://help.galaxyproject.org/t/admin-in-local-installation-impossible-to-make-work/16581)
**Author:** [@Victor\_Martinez](https://help.galaxyproject.org/u/Victor_Martinez)\ **Replies:** 1\ **Last updated:** [December 18, 2025, 6:31am UTC](https://help.galaxyproject.org/t/admin-in-local-installation-impossible-to-make-work/16581 "2025-12-18T06:31:56Z")
Dear all I have been tried several times and using sevreal ways to install ga.laxy locally using admin accounts but it has been impossible. I am using the latest version. Any hints to make it work? the galaxy.yml is: g… --- ## [Searching through Galaxy Libraries and Library Datasets effectively](https://help.galaxyproject.org/t/searching-through-galaxy-libraries-and-library-datasets-effectively/16552)
**Author:** [@JBoom](https://help.galaxyproject.org/u/JBoom)\ **Replies:** 2\ **Last updated:** [December 9, 2025, 9:51am UTC](https://help.galaxyproject.org/t/searching-through-galaxy-libraries-and-library-datasets-effectively/16552 "2025-12-09T09:51:04Z")
Greetings! I was hoping someone could help me with this. In our local Galaxy installment we have made some internal data available to users on a permission basis (using groups and roles) using Galaxy Libraries. In the… --- ## [External tool link: open a new tab](https://help.galaxyproject.org/t/external-tool-link-open-a-new-tab/16522)
**Author:** [@JBoom](https://help.galaxyproject.org/u/JBoom)\ **Replies:** 3\ **Last updated:** [December 8, 2025, 7:45pm UTC](https://help.galaxyproject.org/t/external-tool-link-open-a-new-tab/16522 "2025-12-08T19:45:06Z")
Greetings all! I was hoping a Galaxy admin could help me. Based on examples like: galaxy/tools/data\_source/diced.xml at dev · galaxyproject/galaxy, I have added a tool to our Galaxy instance that runs somewhere else on… --- ## [HUMAnN Cached database with clade-specific marker genes](https://help.galaxyproject.org/t/humann-cached-database-with-clade-specific-marker-genes/11847)
**Author:** [@KaunoSeptintasFortas](https://help.galaxyproject.org/u/KaunoSeptintasFortas)\ **Replies:** 11\ **Last updated:** [December 8, 2025, 6:06pm UTC](https://help.galaxyproject.org/t/humann-cached-database-with-clade-specific-marker-genes/11847 "2025-12-08T18:06:12Z")
Hello, I am trying to run HUMAnN on MetaPhlAn data, but HUMAnN does not recognise Cached database with clade-specific marker genes. How can I install this database? Nukleotide and proteine databases are recognised. Than… --- ## [Change the default Activity Bar view](https://help.galaxyproject.org/t/change-the-default-activity-bar-view/16476)
**Author:** [@JBoom](https://help.galaxyproject.org/u/JBoom)\ **Replies:** 3\ **Last updated:** [November 12, 2025, 1:23pm UTC](https://help.galaxyproject.org/t/change-the-default-activity-bar-view/16476 "2025-11-12T13:23:25Z")
Greetings, I was hoping someone in the Galaxy Admin community could advise me on whether it’s possible to customise the Activity Bar. I’m specifically interested in configuring what users see in their Activity Bar up… --- ## [QIIME 2 installed in Galaxy, but tools not appearing in the left panel (Mac mini M4 & Ubuntu)](https://help.galaxyproject.org/t/qiime-2-installed-in-galaxy-but-tools-not-appearing-in-the-left-panel-mac-mini-m4-ubuntu/16401)
**Author:** [@HKadokawa](https://help.galaxyproject.org/u/HKadokawa)\ **Replies:** 7\ **Last updated:** [November 8, 2025, 3:44pm UTC](https://help.galaxyproject.org/t/qiime-2-installed-in-galaxy-but-tools-not-appearing-in-the-left-panel-mac-mini-m4-ubuntu/16401 "2025-11-08T15:44:49Z")
Hello, Has anyone recently succeeded in setting up a metagenomics analysis environment with Galaxy + QIIME 2? I tried on both a Mac mini M4 (Apple silicon) and a custom-built PC running Ubuntu 22.04. I can install QC-… --- ## [Assistance Required: Missing Tools from Galaxy ToolShed](https://help.galaxyproject.org/t/assistance-required-missing-tools-from-galaxy-toolshed/16455)
**Author:** [@Williams](https://help.galaxyproject.org/u/Williams)\ **Replies:** 1\ **Last updated:** [October 30, 2025, 6:57pm UTC](https://help.galaxyproject.org/t/assistance-required-missing-tools-from-galaxy-toolshed/16455 "2025-10-30T18:57:40Z")
Hello Galaxy Community, I hope this message finds you well. I am currently facing an issue with two tools that are not available on the Galaxy ToolShed, and I would appreciate your guidance or assistance. The specific … --- ## [GATK4 Mutect2 error - SyntaxError - invalid syntax](https://help.galaxyproject.org/t/gatk4-mutect2-error-syntaxerror-invalid-syntax/16450)
**Author:** [@prao123](https://help.galaxyproject.org/u/prao123)\ **Replies:** 1\ **Last updated:** [October 30, 2025, 12:33am UTC](https://help.galaxyproject.org/t/gatk4-mutect2-error-syntaxerror-invalid-syntax/16450 "2025-10-30T00:33:38Z")
Hello, When using GATK4 for a tumour only analysis on a local server, the tool errors out with a “SyntaxError: invalid syntax” error. I have tried different versions of GATK4 Mutect2 (4.1.7.0+galaxy1, 4.1.7.0+galaxy1+ga… --- ## [This job was killed when Galaxy was restarted. Please retry the job](https://help.galaxyproject.org/t/this-job-was-killed-when-galaxy-was-restarted-please-retry-the-job/10650)
**Author:** [@H\_Z](https://help.galaxyproject.org/u/H_Z)\ **Replies:** 11\ **Last updated:** [October 20, 2025, 6:00pm UTC](https://help.galaxyproject.org/t/this-job-was-killed-when-galaxy-was-restarted-please-retry-the-job/10650 "2025-10-20T18:00:39Z")
Hi I’m trying to get data using the local galaxy while the error keeping occurs. Wondering what should I do with that?? --- ## [Bioblend NGINX HTTPS](https://help.galaxyproject.org/t/bioblend-nginx-https/16377)
**Author:** [@breakthewall](https://help.galaxyproject.org/u/breakthewall)\ **Replies:** 7\ **Last updated:** [October 17, 2025, 9:18pm UTC](https://help.galaxyproject.org/t/bioblend-nginx-https/16377 "2025-10-17T21:18:09Z")
Hi, I have a Galaxy instance behind an NGINX reverse-proxy protected by SSL, i.e. HTTPS. I try to use Bioblend to get access to Galaxy through the reverse proxy but I have SSL errors. Python 3.13.7 | packaged by conda… --- ## [Library dataset as input of a workflow](https://help.galaxyproject.org/t/library-dataset-as-input-of-a-workflow/16389)
**Author:** [@breakthewall](https://help.galaxyproject.org/u/breakthewall)\ **Replies:** 3\ **Last updated:** [October 15, 2025, 5:55pm UTC](https://help.galaxyproject.org/t/library-dataset-as-input-of-a-workflow/16389 "2025-10-15T17:55:14Z")
Hi, is it possible to set files from libraries as input dataset of a workflow, I mean in the workflow editor, as fixed parameter? Thanks --- ## [Error parsing the tool configuration /galaxy/config/shed\_tool\_conf.xml](https://help.galaxyproject.org/t/error-parsing-the-tool-configuration-galaxy-config-shed-tool-conf-xml/16373)
**Author:** [@breakthewall](https://help.galaxyproject.org/u/breakthewall)\ **Replies:** 1\ **Last updated:** [October 13, 2025, 3:25pm UTC](https://help.galaxyproject.org/t/error-parsing-the-tool-configuration-galaxy-config-shed-tool-conf-xml/16373 "2025-10-13T15:25:28Z")
Hi, today by restarting my Dockerized Galaxy that worked well so far, I got the following error that lets my instance stucked: … panel\_searches\\\[panel\_view\_id\\\] = ToolPanelViewSearch( … --- ## [Galaxy Job Execution Error with SLURM Setup](https://help.galaxyproject.org/t/galaxy-job-execution-error-with-slurm-setup/16249)
**Author:** [@hohosharon](https://help.galaxyproject.org/u/hohosharon)\ **Replies:** 5\ **Last updated:** [September 21, 2025, 10:10pm UTC](https://help.galaxyproject.org/t/galaxy-job-execution-error-with-slurm-setup/16249 "2025-09-21T22:10:47Z")
Dear Galaxy Team, I am setting up Galaxy v25 on my local VM in a shared HPC environment. However, I encountered an error related to the SLURM setup in my job\_conf.yml. Below are the relevant excerpts and error messages: … --- ## [How to configure SLURM queues (short/medium/long) for Galaxy on HPC?](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254)
**Author:** [@Mohanchaitanya](https://help.galaxyproject.org/u/Mohanchaitanya)\ **Replies:** 1\ **Last updated:** [September 15, 2025, 10:34pm UTC](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254 "2025-09-15T22:34:53Z")
Hello, I am new to running Galaxy on our Institute’s HPC. Our cluster uses SLURM with three partitions: Short: 2 hours, 128 cores max, 2 nodes max, with high priority to run the job. Medium: 72 hours, 192 cores ma… --- ## [How to install kraken2 database](https://help.galaxyproject.org/t/how-to-install-kraken2-database/12573)
**Author:** [@Anik\_Du](https://help.galaxyproject.org/u/Anik_Du)\ **Replies:** 5\ **Last updated:** [June 5, 2024, 10:26pm UTC](https://help.galaxyproject.org/t/how-to-install-kraken2-database/12573 "2024-06-05T22:26:57Z")
Hello, I have installed Galaxy locally using Galaxy Helm chart from here: \[GitHub - galaxyproject/galaxy-helm: Minimal setup required to run Galaxy under Kubernetes · GitHub\] I have installed Kraken, Kraken2, and other… --- ## [Trouble Uploading Files to Local Galaxy v25 on Shared HPC](https://help.galaxyproject.org/t/trouble-uploading-files-to-local-galaxy-v25-on-shared-hpc/16235)
**Author:** [@hohosharon](https://help.galaxyproject.org/u/hohosharon)\ **Replies:** 2\ **Last updated:** [September 6, 2025, 3:45am UTC](https://help.galaxyproject.org/t/trouble-uploading-files-to-local-galaxy-v25-on-shared-hpc/16235 "2025-09-06T03:45:03Z")
Hi everyone, I recently set up a local Galaxy v25 instance on a VM in a shared HPC environment. However, I am unable to upload any files to this Galaxy instance. When I try to upload a file, the upload tool keeps showi… --- ## [Install on VMs with and without graphics accelerators](https://help.galaxyproject.org/t/install-on-vms-with-and-without-graphics-accelerators/16219)
**Author:** [@GaryAitken](https://help.galaxyproject.org/u/GaryAitken)\ **Replies:** 2\ **Last updated:** [August 29, 2025, 10:10pm UTC](https://help.galaxyproject.org/t/install-on-vms-with-and-without-graphics-accelerators/16219 "2025-08-29T22:10:34Z")
Can the same process be used to build a galaxy installation on a VM with graphics accelerator hardware as that for non-graphics accelerator hardware? In other words, if I build a test installation on non-graphics enable… --- ## [Random empty output files](https://help.galaxyproject.org/t/random-empty-output-files/16169)
**Author:** [@Koen\_Nijbroek](https://help.galaxyproject.org/u/Koen_Nijbroek)\ **Replies:** 7\ **Last updated:** [August 26, 2025, 5:08pm UTC](https://help.galaxyproject.org/t/random-empty-output-files/16169 "2025-08-26T17:08:46Z")
Hi, I’m running a private instance of the latest Galaxy helm chart on Kubernetes. Whenever I run tools of which one of the inputs is a collection of files I experience that the outputs in the interface can be empty wher… --- ## [Planemo, docker, python: issue with getting args passed to the script](https://help.galaxyproject.org/t/planemo-docker-python-issue-with-getting-args-passed-to-the-script/16172)
**Author:** [@4urelie](https://help.galaxyproject.org/u/4urelie)\ **Replies:** 5\ **Last updated:** [August 19, 2025, 8:09am UTC](https://help.galaxyproject.org/t/planemo-docker-python-issue-with-getting-args-passed-to-the-script/16172 "2025-08-19T08:09:30Z")
Hi all, I am working on my first galaxy tool release (private tool, so I made some minimal code that reproduces my issue), and I am struggling with passing python args; when I print the sys.argv content before parsing a… [Next page](https://help.galaxyproject.org/tag/galaxy-local/58.md?match_all_tags=true&page=1&tags%5B%5D=galaxy-local)