# \#tool-request **URL:** https://help.galaxyproject.org/tag/tool-request/231.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [MrBayes consensus tree file not shown in output](https://help.galaxyproject.org/t/mrbayes-consensus-tree-file-not-shown-in-output/18221)
**Author:** [@tavovato](https://help.galaxyproject.org/u/tavovato)\ **Replies:** 2\ **Last updated:** [July 30, 2026, 9:52pm UTC](https://help.galaxyproject.org/t/mrbayes-consensus-tree-file-not-shown-in-output/18221 "2026-07-30T21:52:26Z")
Hi! I ran a MrBayes analysis on usegalaxy.eu and the job seems to have completed successfully. The summary report indicates that several MrBayes output files were generated, including .run1.t, .run2.t, .pstat, .tstat, .… --- ## [MrBayes - no output files found](https://help.galaxyproject.org/t/mrbayes-no-output-files-found/16275)
**Author:** [@Alan\_Thomas](https://help.galaxyproject.org/u/Alan_Thomas)\ **Replies:** 4\ **Last updated:** [July 30, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/mrbayes-no-output-files-found/16275 "2026-07-30T18:12:31Z")
Hai After analysing data using MrBayes in https://usegalaxy.eu/, output files are not created. No output files found. Only a text file was found. Could you please help me? Thank you. --- ## [Request: Add host-decontamination tool (KneadData) or a comparable tool on Galaxy.eu for human shotgun metagenomics preprocessing](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472)
**Author:** [@sri\_microbiome](https://help.galaxyproject.org/u/sri_microbiome)\ **Replies:** 2\ **Last updated:** [November 6, 2025, 7:23am UTC](https://help.galaxyproject.org/t/request-add-host-decontamination-tool-kneaddata-or-a-comparable-tool-on-galaxy-eu-for-human-shotgun-metagenomics-preprocessing/16472 "2025-11-06T07:23:38Z")
Hello Support Team, I plan to pre- process human stool shotgun metagenomes on Galaxy.eu and need a host-decontamination step before MetaPhlAn/HUMAnN. I couldn’t find KneadData in the tool panel,so I can’t filter human r… --- ## [Can you provide installation tools（FPKM/TPM/CPM Calculator，Merge RNA-seq Counts） for Galaxy 25.0? Thank you!](https://help.galaxyproject.org/t/can-you-provide-installation-tools-fpkm-tpm-cpm-calculator-merge-rna-seq-counts-for-galaxy-25-0-thank-you/16381)
**Author:** [@fengtong2018](https://help.galaxyproject.org/u/fengtong2018)\ **Replies:** 3\ **Last updated:** [October 15, 2025, 6:22pm UTC](https://help.galaxyproject.org/t/can-you-provide-installation-tools-fpkm-tpm-cpm-calculator-merge-rna-seq-counts-for-galaxy-25-0-thank-you/16381 "2025-10-15T18:22:45Z")
Can you provide installation tools for Galaxy 25.0? Thank you! FPKM/TPM/CPM Calculator，Merge RNA-seq Counts --- ## [New wrapped tool request for the IUC or Finding existing wrapped tools. Example: genome scaffolder](https://help.galaxyproject.org/t/new-wrapped-tool-request-for-the-iuc-or-finding-existing-wrapped-tools-example-genome-scaffolder/2111)
**Author:** [@Rahul\_Shelke](https://help.galaxyproject.org/u/Rahul_Shelke)\ **Replies:** 9\ **Last updated:** [October 15, 2025, 6:12pm UTC](https://help.galaxyproject.org/t/new-wrapped-tool-request-for-the-iuc-or-finding-existing-wrapped-tools-example-genome-scaffolder/2111 "2025-10-15T18:12:49Z")
Can I request Genome scaffolder on galaxy? --- ## [Cannot access Crispresso2 tool from usegalaxy.org](https://help.galaxyproject.org/t/cannot-access-crispresso2-tool-from-usegalaxy-org/14727)
**Author:** [@Maddy-UW](https://help.galaxyproject.org/u/Maddy-UW)\ **Replies:** 3\ **Last updated:** [February 13, 2025, 11:59pm UTC](https://help.galaxyproject.org/t/cannot-access-crispresso2-tool-from-usegalaxy-org/14727 "2025-02-13T23:59:45Z")
Hello! I have been trying to access the Crispresso2 tool from usegalaxy.org server but it says no result found when I type in the tool name in the Tools search bar. Could someone direct me on how I can use this tool? (I … --- ## [updating eggnog software and database](https://help.galaxyproject.org/t/updating-eggnog-software-and-database/14487)
**Author:** [@krabapple](https://help.galaxyproject.org/u/krabapple)\ **Replies:** 1\ **Last updated:** [January 22, 2025, 12:19am UTC](https://help.galaxyproject.org/t/updating-eggnog-software-and-database/14487 "2025-01-22T00:19:56Z")
I notice, on every Galaxy server I checked, that they use v2.1.8 of eggnog-mapper and v5 of the database, e.g. usegalaxy.eu uses: toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog\_mapper/eggnog\_mapper/2.1.8+galaxy4 eggnog da… --- ## [Kraken-mpa-report and Kraken2](https://help.galaxyproject.org/t/kraken-mpa-report-and-kraken2/12988)
**Author:** [@Yordan\_Hodzhev](https://help.galaxyproject.org/u/Yordan_Hodzhev)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 8:46pm UTC](https://help.galaxyproject.org/t/kraken-mpa-report-and-kraken2/12988 "2024-07-17T20:46:34Z")
Could you, please update the database definitions оф тхе Kraken-mpa-report, so that they correspond to Kraken2 tool? --- ## [Bracken reference databases update request in order to cover options provided by Kraken2](https://help.galaxyproject.org/t/bracken-reference-databases-update-request-in-order-to-cover-options-provided-by-kraken2/12974)
**Author:** [@Yordan\_Hodzhev](https://help.galaxyproject.org/u/Yordan_Hodzhev)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 4:02pm UTC](https://help.galaxyproject.org/t/bracken-reference-databases-update-request-in-order-to-cover-options-provided-by-kraken2/12974 "2024-07-17T16:02:47Z")
Dear Admins, Could you please update the list of Kmer distribution reference databases for Bracken tool as it is currently in Kraken2 (Galaxy Version 2.1.3+galaxy1): Thus, users can recalculate in Bracken all kinds o… --- ## [adding a new pipeline on usegalaxy.org](https://help.galaxyproject.org/t/adding-a-new-pipeline-on-usegalaxy-org/12386)
**Author:** [@Josh](https://help.galaxyproject.org/u/Josh)\ **Replies:** 4\ **Last updated:** [May 3, 2024, 5:20pm UTC](https://help.galaxyproject.org/t/adding-a-new-pipeline-on-usegalaxy-org/12386 "2024-05-03T17:20:02Z")
I am wondering if there is a way to request an addition of a new pipeline for usegalaxy.org I am planning to do circular RNA analysis and found that usegalaxy.eu has circExplorer 2, but usegalaxy.org doesn’t. Since my m… --- ## [Request installation of the following tools:](https://help.galaxyproject.org/t/request-installation-of-the-following-tools/11165)
**Author:** [@tann5er](https://help.galaxyproject.org/u/tann5er)\ **Replies:** 1\ **Last updated:** [November 17, 2023, 9:53pm UTC](https://help.galaxyproject.org/t/request-installation-of-the-following-tools/11165 "2023-11-17T21:53:30Z")
Hi there Could I please request the installation of the following tools: --- ## [MAGenTA Not Available?](https://help.galaxyproject.org/t/magenta-not-available/7743)
**Author:** [@Shalee\_Carlson](https://help.galaxyproject.org/u/Shalee_Carlson)\ **Replies:** 1\ **Last updated:** [March 25, 2022, 8:49am UTC](https://help.galaxyproject.org/t/magenta-not-available/7743 "2022-03-25T08:49:04Z")
I recently came across the article " MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization" which says the tool MAGenTA is available in the Galaxy PublicToolShed, but I can’t seem to find… --- ## [how to set up user defined size factor in Deseq2](https://help.galaxyproject.org/t/how-to-set-up-user-defined-size-factor-in-deseq2/7593)
**Author:** [@Cindy](https://help.galaxyproject.org/u/Cindy)\ **Replies:** 1\ **Last updated:** [February 25, 2022, 4:57pm UTC](https://help.galaxyproject.org/t/how-to-set-up-user-defined-size-factor-in-deseq2/7593 "2022-02-25T16:57:23Z")
Hi~ I see Deseq2 (Galaxy Version 2.11.40.7+galaxy1) added the “size factor” option in output, rather than version 2.11.40.6, which is a big improvement for me. Further more, I wonder could we have the option to use custo… --- ## [Pindel in usegalaxy](https://help.galaxyproject.org/t/pindel-in-usegalaxy/2212)
**Author:** [@Athina](https://help.galaxyproject.org/u/Athina)\ **Replies:** 4\ **Last updated:** [October 29, 2020, 8:28am UTC](https://help.galaxyproject.org/t/pindel-in-usegalaxy/2212 "2020-10-29T08:28:48Z")
Hi, I want to run Pindel on galaxy but it doesn’t seem to pre-exist in the tools. Is there a way to add it in? Thanks! --- ## [CollectHsMetrics (Picard)](https://help.galaxyproject.org/t/collecthsmetrics-picard/1244)
**Author:** [@delphineboulet](https://help.galaxyproject.org/u/delphineboulet)\ **Replies:** 1\ **Last updated:** [May 6, 2019, 6:16pm UTC](https://help.galaxyproject.org/t/collecthsmetrics-picard/1244 "2019-05-06T18:16:46Z")
Hello, I am using galaxy.org and I am searching the tool: CollectHsMetrics (Picard). I don’t find it. How can I make it appear into the tool list? thanks delphine