# \#data-manager **URL:** https://help.galaxyproject.org/tag/data-manager/60.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Troubleshooting the Kraken2 Data Manager and CVMFS indes](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256)
**Author:** [@Chetan\_Mahale](https://help.galaxyproject.org/u/Chetan_Mahale)\ **Replies:** 1\ **Last updated:** [September 15, 2025, 10:53pm UTC](https://help.galaxyproject.org/t/troubleshooting-the-kraken2-data-manager-and-cvmfs-indes/16256 "2025-09-15T22:53:12Z")
Hi All, I wanted to install Galaxy server on my local hosting using ubuntu server. I wanted to scan the fungi data files for its classification. Can any one please provide a script which can do the galaxy installation an… --- ## [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… --- ## [Data manager for virhunter](https://help.galaxyproject.org/t/data-manager-for-virhunter/15685)
**Author:** [@ccoulombe](https://help.galaxyproject.org/u/ccoulombe)\ **Replies:** 3\ **Last updated:** [July 23, 2025, 7:07pm UTC](https://help.galaxyproject.org/t/data-manager-for-virhunter/15685 "2025-07-23T19:07:11Z")
Hello! On the Canadian usegalaxy instance (.ca), the tool virhunter is available but there’s no associated data manager (that I could find). I noticed the tool is also available on .eu instance, with the local datasets… --- ## [Data Manager for blastdb](https://help.galaxyproject.org/t/data-manager-for-blastdb/14803)
**Author:** [@hughesd](https://help.galaxyproject.org/u/hughesd)\ **Replies:** 1\ **Last updated:** [February 20, 2025, 8:23pm UTC](https://help.galaxyproject.org/t/data-manager-for-blastdb/14803 "2025-02-20T20:23:09Z")
We could not find a Data Manager to populate the Tool Data Tables “blastdb” and “blastdb\_p”. Is this something we must do manually? My guess is that we should add entries to ../tool\_data/toolshed.g2.bx.psu.edu/repos/d… --- ## [Remove entries in Data Manager: all\_fasta.](https://help.galaxyproject.org/t/remove-entries-in-data-manager-all-fasta/14705)
**Author:** [@hughesd](https://help.galaxyproject.org/u/hughesd)\ **Replies:** 4\ **Last updated:** [February 20, 2025, 11:47am UTC](https://help.galaxyproject.org/t/remove-entries-in-data-manager-all-fasta/14705 "2025-02-20T11:47:40Z")
I am an admin on a local instance, trouble-shooting problems with using DataManager. Is it possible to remove entries in Data Manager, specifically all\_fasta? I found an old post which says No. Is this still the case? … --- ## [Pharokka Database](https://help.galaxyproject.org/t/pharokka-database/9830)
**Author:** [@gbouras13](https://help.galaxyproject.org/u/gbouras13)\ **Replies:** 10\ **Last updated:** [January 2, 2025, 2:02am UTC](https://help.galaxyproject.org/t/pharokka-database/9830 "2025-01-02T02:02:52Z")
Hi, I am the developer of Pharokka and am trying to use Pharokka v 1.2.1 on the EU server (the adding of this to the toolshed was extremely helpfully handled by Paul Zierep! thanks Paul!) When I go to run Pharokka, the… --- ## [Remove installed databases](https://help.galaxyproject.org/t/remove-installed-databases/13203)
**Author:** [@Shreyash\_04](https://help.galaxyproject.org/u/Shreyash_04)\ **Replies:** 2\ **Last updated:** [August 14, 2024, 12:52pm UTC](https://help.galaxyproject.org/t/remove-installed-databases/13203 "2024-08-14T12:52:23Z")
Dear Galaxy team, I would like to remove installed databases for a tool (BAKTA) from our local galaxy server. Same database was installed in duplicates leading to error in the tool. Hence, we would like to remove the in… --- ## [Use Create DBKey and Reference Genome to define new entries](https://help.galaxyproject.org/t/use-create-dbkey-and-reference-genome-to-define-new-entries/13163)
**Author:** [@frans](https://help.galaxyproject.org/u/frans)\ **Replies:** 5\ **Last updated:** [August 13, 2024, 6:07pm UTC](https://help.galaxyproject.org/t/use-create-dbkey-and-reference-genome-to-define-new-entries/13163 "2024-08-13T18:07:18Z")
Error adding new builds after adding cmvfs tool\_data\_tables. I’ve used both release\_24.1 and release\_23.0 and for both versions after adding the line that defines the external tool\_data\_tables in the galaxy config secti… --- ## [funannotate data manager error url not found](https://help.galaxyproject.org/t/funannotate-data-manager-error-url-not-found/12815)
**Author:** [@sebibarLE](https://help.galaxyproject.org/u/sebibarLE)\ **Replies:** 1\ **Last updated:** [July 5, 2024, 7:42pm UTC](https://help.galaxyproject.org/t/funannotate-data-manager-error-url-not-found/12815 "2024-07-05T19:42:02Z")
When I run the funannotate data manager most databases can be downloaded but with a certain file the URL cannot be found: requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/… --- ## [Freebayes errors out in v. 1.3.6 vs 1.3.1](https://help.galaxyproject.org/t/freebayes-errors-out-in-v-1-3-6-vs-1-3-1/9186)
**Author:** [@prao123](https://help.galaxyproject.org/u/prao123)\ **Replies:** 4\ **Last updated:** [December 16, 2022, 4:54pm UTC](https://help.galaxyproject.org/t/freebayes-errors-out-in-v-1-3-6-vs-1-3-1/9186 "2022-12-16T16:54:39Z")
Hello, I have recently installed a local version of Galaxy and installed FreeBayes 1.3.6 from the tool shed. After indexing the genomes hg19 and hg38 as explained in many posts, I ran HiSat2 to generate the BAM files fo… --- ## [gemini database download error](https://help.galaxyproject.org/t/gemini-database-download-error/9087)
**Author:** [@apolitics](https://help.galaxyproject.org/u/apolitics)\ **Replies:** 3\ **Last updated:** [November 28, 2022, 3:50pm UTC](https://help.galaxyproject.org/t/gemini-database-download-error/9087 "2022-11-28T15:50:54Z")
Hello, I have tried to download gemini database through the gemini data manager, and encountered an error related… After everything has been downloaded… it seems like python script failed… There were no options t… --- ## [Creating a customized genome index (large) on a private Galaxy server -\> Use Data Managers](https://help.galaxyproject.org/t/creating-a-customized-genome-index-large-on-a-private-galaxy-server-use-data-managers/8499)
**Author:** [@kdwyer](https://help.galaxyproject.org/u/kdwyer)\ **Replies:** 3\ **Last updated:** [August 23, 2022, 12:06am UTC](https://help.galaxyproject.org/t/creating-a-customized-genome-index-large-on-a-private-galaxy-server-use-data-managers/8499 "2022-08-23T00:06:35Z")
Hello, I was hoping to get some advice - I am trying to create a custom genome with combine human and rat builds to use as a reference genome for alignment with bulk RNA sequencing data. I am trying to use the UCSC data… --- ## [No options available (Select Reference Genome)](https://help.galaxyproject.org/t/no-options-available-select-reference-genome/8193)
**Author:** [@cw951](https://help.galaxyproject.org/u/cw951)\ **Replies:** 3\ **Last updated:** [June 14, 2022, 7:38pm UTC](https://help.galaxyproject.org/t/no-options-available-select-reference-genome/8193 "2022-06-14T19:38:10Z")
Hi everyone, We recently installed the Galaxy Server to our mainframe. However, we are having difficulty in using RNA STAR as there is no reference genome available (see attached picture). How can we rectify this? M… --- ## [Connection timed out error while running data\_manager\_fetch\_genome\_dbkeys\_all\_fasta](https://help.galaxyproject.org/t/connection-timed-out-error-while-running-data-manager-fetch-genome-dbkeys-all-fasta/7241)
**Author:** [@syliang18](https://help.galaxyproject.org/u/syliang18)\ **Replies:** 1\ **Last updated:** [January 6, 2022, 7:53pm UTC](https://help.galaxyproject.org/t/connection-timed-out-error-while-running-data-manager-fetch-genome-dbkeys-all-fasta/7241 "2022-01-06T19:53:36Z")
Dear all, I have a local Galaxy v 21.09 installed on a server and would like to build a reference genome using data\_manager\_fetch\_genome\_dbkeys\_all\_fasta by following the reference at https://biostar.galaxyproject.org/p… --- ## [Building an indexed genome file for GATK tools](https://help.galaxyproject.org/t/building-an-indexed-genome-file-for-gatk-tools/4529)
**Author:** [@jsalem](https://help.galaxyproject.org/u/jsalem)\ **Replies:** 13\ **Last updated:** [October 27, 2021, 8:00pm UTC](https://help.galaxyproject.org/t/building-an-indexed-genome-file-for-gatk-tools/4529 "2021-10-27T20:00:29Z")
Hi, Does anyone have any pointers for indexing a reference sequence for use with GATK tools? I have indexed reference sequences that I use for BWA and minimap2, but I can’t get the reference sequences to appear with GAT… --- ## [Delete data created with data manager?](https://help.galaxyproject.org/t/delete-data-created-with-data-manager/6924)
**Author:** [@wormball](https://help.galaxyproject.org/u/wormball)\ **Replies:** 1\ **Last updated:** [October 26, 2021, 4:04pm UTC](https://help.galaxyproject.org/t/delete-data-created-with-data-manager/6924 "2021-10-26T16:04:01Z")
Hello! How can i delete data created with data manager? Thanks in advance. --- ## [Any way to align a single cDNA sequence against the raw nanopore data?](https://help.galaxyproject.org/t/any-way-to-align-a-single-cdna-sequence-against-the-raw-nanopore-data/6919)
**Author:** [@daikez](https://help.galaxyproject.org/u/daikez)\ **Replies:** 2\ **Last updated:** [October 25, 2021, 11:22am UTC](https://help.galaxyproject.org/t/any-way-to-align-a-single-cdna-sequence-against-the-raw-nanopore-data/6919 "2021-10-25T11:22:40Z")
Hi, I am trying to check if my interested target gene (GenBank cDNA entry) exists in the raw nanpore sequencing data. I have tried to use minimap2 to compare one cDNA against the fastq format raw data and returned with s… --- ## [Gaps in the genome assembly](https://help.galaxyproject.org/t/gaps-in-the-genome-assembly/6603)
**Author:** [@daikez](https://help.galaxyproject.org/u/daikez)\ **Replies:** 0\ **Last updated:** [August 31, 2021, 6:45am UTC](https://help.galaxyproject.org/t/gaps-in-the-genome-assembly/6603 "2021-08-31T06:45:29Z")
Hi, I found some obvious gaps in my assembly. My estimation is 50~100 kb of gap from each side of the existing contigs and the size of the total uncertain region is around 300 kb. Although it is not very big gap compare… --- ## [Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting](https://help.galaxyproject.org/t/indexing-reference-genomes-with-data-managers-resources-tutorials-troubleshooting/1223)
**Author:** [@asta](https://help.galaxyproject.org/u/asta)\ **Replies:** 28\ **Last updated:** [July 7, 2021, 2:43pm UTC](https://help.galaxyproject.org/t/indexing-reference-genomes-with-data-managers-resources-tutorials-troubleshooting/1223 "2021-07-07T14:43:44Z")
Hi, I’m attempting to run HISAT2 on paired RNAseq data. I have run it successfully previously on the main server using the mm10 built-in reference genome, however, I am now using a local server and the built-in referenc… --- ## [Setting a custom database input for tools -- in a workflow or on a tool form](https://help.galaxyproject.org/t/setting-a-custom-database-input-for-tools-in-a-workflow-or-on-a-tool-form/6207)
**Author:** [@wormball](https://help.galaxyproject.org/u/wormball)\ **Replies:** 8\ **Last updated:** [June 23, 2021, 2:55pm UTC](https://help.galaxyproject.org/t/setting-a-custom-database-input-for-tools-in-a-workflow-or-on-a-tool-form/6207 "2021-06-23T14:55:05Z")
Hello! My workflow requires to upload and select “hg38.analysisSet.fa” every time i run it. But it is waste of time cos this file is already on the server and hardcoded into plenty of our tool xmls anyway, and only Merg… --- ## [Can't use Bowtie2 index builder - "Requested version unavailable" error](https://help.galaxyproject.org/t/cant-use-bowtie2-index-builder-requested-version-unavailable-error/6055)
**Author:** [@phagepower](https://help.galaxyproject.org/u/phagepower)\ **Replies:** 3\ **Last updated:** [June 14, 2021, 6:21pm UTC](https://help.galaxyproject.org/t/cant-use-bowtie2-index-builder-requested-version-unavailable-error/6055 "2021-06-14T18:21:16Z")
Hi, I installed the Bowtie2 index builder/data manager from the toolshed (Galaxy | Tool Shed) however whenever I open it, I get the “Requested version unavailable” error at the top, and cannot select any FASTA files as … --- ## [Extract a subsequence from the whole genome assembly?](https://help.galaxyproject.org/t/extract-a-subsequence-from-the-whole-genome-assembly/6162)
**Author:** [@daikez](https://help.galaxyproject.org/u/daikez)\ **Replies:** 11\ **Last updated:** [June 11, 2021, 2:19pm UTC](https://help.galaxyproject.org/t/extract-a-subsequence-from-the-whole-genome-assembly/6162 "2021-06-11T14:19:11Z")
I have managed to map my interested gene region against my home built whole genome assembly. So I saw the results has returned a best matched scaffold id. So if it is possible to extract the target scaffold sequence out … --- ## [Alternative to DM tools for inbuilt reference sequence](https://help.galaxyproject.org/t/alternative-to-dm-tools-for-inbuilt-reference-sequence/2967)
**Author:** [@YKV](https://help.galaxyproject.org/u/YKV)\ **Replies:** 3\ **Last updated:** [November 30, 2020, 9:15pm UTC](https://help.galaxyproject.org/t/alternative-to-dm-tools-for-inbuilt-reference-sequence/2967 "2020-11-30T21:15:06Z")
Hi, Is there any other way other than managing DM Tools for the inbuilt reference genome sequence. I have found couple questions and answers and related links for the above task. All it says about DM tools. https://bi… --- ## [Baboon reference genome](https://help.galaxyproject.org/t/baboon-reference-genome/4731)
**Author:** [@Adekunbi123456](https://help.galaxyproject.org/u/Adekunbi123456)\ **Replies:** 2\ **Last updated:** [October 30, 2020, 9:40am UTC](https://help.galaxyproject.org/t/baboon-reference-genome/4731 "2020-10-30T09:40:45Z")
Apologies for asking an obvious question. Please how do I correctly download the FASTA copy of the baboon reference genome on NCBI link below; https://www.ncbi.nlm.nih.gov/genome/assembly/1082401 I used the download a… --- ## [BWA-MEM Index Error - fail to open file](https://help.galaxyproject.org/t/bwa-mem-index-error-fail-to-open-file/2050)
**Author:** [@incho](https://help.galaxyproject.org/u/incho)\ **Replies:** 1\ **Last updated:** [September 24, 2020, 10:25pm UTC](https://help.galaxyproject.org/t/bwa-mem-index-error-fail-to-open-file/2050 "2020-09-24T22:25:02Z")
Hello, I am pretty new here, and I sincerely apologize if this is a duplicate question. I tried to search for this for two days but did not find a similar topic here. I recently set up a local Galaxy Serve on my office… --- ## [Galaxy can't find custom blast db](https://help.galaxyproject.org/t/galaxy-cant-find-custom-blast-db/4009)
**Author:** [@KeelyDulmage](https://help.galaxyproject.org/u/KeelyDulmage)\ **Replies:** 2\ **Last updated:** [June 30, 2020, 12:19pm UTC](https://help.galaxyproject.org/t/galaxy-cant-find-custom-blast-db/4009 "2020-06-30T12:19:40Z")
I’m trying to install a custom blast db into a locally hosted instance of Galaxy. I have edited the blastdb.loc file and it is properly detected by Galaxy, as seen in the admin datatable: The file path points to a f… --- ## [Fatal error: Exit code 1 () when using SAM FASTA Index Builder.](https://help.galaxyproject.org/t/fatal-error-exit-code-1-when-using-sam-fasta-index-builder/3116)
**Author:** [@Ste92](https://help.galaxyproject.org/u/Ste92)\ **Replies:** 2\ **Last updated:** [March 3, 2020, 5:46pm UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-when-using-sam-fasta-index-builder/3116 "2020-03-03T17:46:15Z")
Hi, I am relatively new to using Galaxy, and I am attempting to try to eventually align my paired RNAseq data using STAR. I am currently running Galaxy (version 19.09) from a personal computer using a University open lo… --- ## [Reference Genome in some tools - Fully indexing genomes with Data Managers](https://help.galaxyproject.org/t/reference-genome-in-some-tools-fully-indexing-genomes-with-data-managers/2850)
**Author:** [@tomlodz](https://help.galaxyproject.org/u/tomlodz)\ **Replies:** 3\ **Last updated:** [January 27, 2020, 6:24am UTC](https://help.galaxyproject.org/t/reference-genome-in-some-tools-fully-indexing-genomes-with-data-managers/2850 "2020-01-27T06:24:21Z")
Hello, I started a local galaxy on a local server. I was able to insert the local reference genomes for mapping in Bowtie2 and BWA-MEM along with doing indexes for it. Mapping works great and without problems. I wanted… --- ## [rsync error on syncing my local galaxy with rsync g2 data manager](https://help.galaxyproject.org/t/rsync-error-on-syncing-my-local-galaxy-with-rsync-g2-data-manager/2572)
**Author:** [@duv\_vayu](https://help.galaxyproject.org/u/duv_vayu)\ **Replies:** 2\ **Last updated:** [December 7, 2019, 9:10am UTC](https://help.galaxyproject.org/t/rsync-error-on-syncing-my-local-galaxy-with-rsync-g2-data-manager/2572 "2019-12-07T09:10:05Z")
it happens on rsyncing blastdb in rsync with g2 also with any other database Error in ‘Rsync with g2’ hook ‘exec\_before\_job’, original message: ‘NoneType’ object has no attribute ‘get\_tool\_relative\_path’ --- ## [Picard indexer (Fatal error: Exit code 1)](https://help.galaxyproject.org/t/picard-indexer-fatal-error-exit-code-1/2527)
**Author:** [@asta](https://help.galaxyproject.org/u/asta)\ **Replies:** 2\ **Last updated:** [November 28, 2019, 8:23pm UTC](https://help.galaxyproject.org/t/picard-indexer-fatal-error-exit-code-1/2527 "2019-11-28T20:23:31Z")
Hi, I’m writing as I’m attempting to import a reference genome into my Galaxy server, which has previously been successful, however, when reaching the step where Picard Indexing has to occur I’m running into an error. S… [Next page](https://help.galaxyproject.org/tag/data-manager/60.md?match_all_tags=true&page=1&tags%5B%5D=data-manager)