Autoupdate tool blog post

Author: UseGalaxy.EU Jenkins Bot

_posts/2026-04-05-tool-update.md

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+---
+site: freiburg
+tags: [tools]
+title: UseGalaxy.eu Tool Updates for 2026-04-05
+supporters:
+- denbi
+- elixir
+---
+
+On 2026-04-05, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #574](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#574/)
+
+
+## Quality Control
+
+- multiqc was updated to [3dd49be3f7d3](https://toolshed.g2.bx.psu.edu/view/iuc/multiqc/3dd49be3f7d3)
+
+## Computer Vision
+
+- sam3_semantic_segmentation was updated to [0bc5b1bfa81a](https://toolshed.g2.bx.psu.edu/view/ecology/sam3_semantic_segmentation/0bc5b1bfa81a)
+
+## Metagenomic Analysis
+
+- genomad_end_to_end was updated to [b405bd1eff93](https://toolshed.g2.bx.psu.edu/view/ufz/genomad_end_to_end/b405bd1eff93)
+
+## Statistics
+
+- saqc was updated to [9e5eb2e6c614](https://toolshed.g2.bx.psu.edu/view/ufz/saqc/9e5eb2e6c614)
+
+## QIIME 2
+
+- qiime2__deblur__denoise_16S was updated to [2572fc0f88f2](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2)
+- qiime2__deblur__denoise_16S was updated to [b883cbea5623](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623)
+
+## Convert Formats
+
+- msconvert was updated to [8edfcbf32616](https://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert/8edfcbf32616)
+
+## Proteomics
+
+- maxquant was updated to [022e886e8f94](https://toolshed.g2.bx.psu.edu/view/galaxyp/maxquant/022e886e8f94)
+- peptideshaker was updated to [c9b13d4069c8](https://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker/c9b13d4069c8)
+
+## Imaging
+
+- split_image was updated to [7191fd16988f](https://toolshed.g2.bx.psu.edu/view/imgteam/split_image/7191fd16988f)
+
+## Annotation
+
+- glimmer_acgt_content was updated to [0d457c894b9f](https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_acgt_content/0d457c894b9f)
+- glimmer_extract was updated to [81d0b66990d2](https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_extract/81d0b66990d2)
+- glimmer_gbk_to_orf was updated to [44dc09edd97b](https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gbk_to_orf/44dc09edd97b)
+- glimmer_long_orfs was updated to [d5b3e82a979f](https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_long_orfs/d5b3e82a979f)
+- angsd was updated to [7b0e59047b2f](https://toolshed.g2.bx.psu.edu/view/iuc/angsd/7b0e59047b2f)
+- bctools_convert_to_binary_barcode was updated to [4f4c5a4dda59](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_convert_to_binary_barcode/4f4c5a4dda59)
+- bctools_extract_alignment_ends was updated to [0be29a221b16](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_extract_alignment_ends/0be29a221b16)
+- bctools_extract_barcodes was updated to [ceb779d5be5b](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_extract_barcodes/ceb779d5be5b)
+- bctools_extract_crosslinked_nucleotides was updated to [12a5e6fa850e](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_extract_crosslinked_nucleotides/12a5e6fa850e)
+- bctools_merge_pcr_duplicates was updated to [04e67d8245fe](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_merge_pcr_duplicates/04e67d8245fe)
+- bctools_remove_spurious_events was updated to [308ab6387c75](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_remove_spurious_events/308ab6387c75)
+- bctools_remove_tail was updated to [6979701451c3](https://toolshed.g2.bx.psu.edu/view/iuc/bctools_remove_tail/6979701451c3)
+- bicodon_counts_from_fasta was updated to [e13169dca7c8](https://toolshed.g2.bx.psu.edu/view/iuc/bicodon_counts_from_fasta/e13169dca7c8)
+- codon_freq_from_bicodons was updated to [cc5a776acd47](https://toolshed.g2.bx.psu.edu/view/iuc/codon_freq_from_bicodons/cc5a776acd47)
+- find_nested_alt_orfs was updated to [14f4c7a8a962](https://toolshed.g2.bx.psu.edu/view/iuc/find_nested_alt_orfs/14f4c7a8a962)
+- hicstuff_pipeline was updated to [7ffc3748ffde](https://toolshed.g2.bx.psu.edu/view/iuc/hicstuff_pipeline/7ffc3748ffde)
+- mist_call was updated to [e4579b48d9ab](https://toolshed.g2.bx.psu.edu/view/iuc/mist_call/e4579b48d9ab)
+- mist_dists was updated to [372a2ff0e14d](https://toolshed.g2.bx.psu.edu/view/iuc/mist_dists/372a2ff0e14d)
+- neighbors was updated to [e06a5c9e97e2](https://toolshed.g2.bx.psu.edu/view/iuc/neighbors/e06a5c9e97e2)
+- psauron was updated to [085451872bcc](https://toolshed.g2.bx.psu.edu/view/iuc/psauron/085451872bcc)
+- sexdeterrmine was updated to [cf3d9775d7ae](https://toolshed.g2.bx.psu.edu/view/iuc/sexdeterrmine/cf3d9775d7ae)
+- tb_profiler_profile was updated to [97a96d2ce8ea](https://toolshed.g2.bx.psu.edu/view/iuc/tb_profiler_profile/97a96d2ce8ea)
+- ucsc_maffilter was updated to [fb6c3ba3a084](https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_maffilter/fb6c3ba3a084)
+
+## Assembly
+
+- vgp_chromosome_assignment was updated to [8926e6cd9071](https://toolshed.g2.bx.psu.edu/view/iuc/vgp_chromosome_assignment/8926e6cd9071)
+- vgp_sak_generation was updated to [8fbdd799f24c](https://toolshed.g2.bx.psu.edu/view/iuc/vgp_sak_generation/8fbdd799f24c)
+- vgp_split_agp was updated to [da61829dc3be](https://toolshed.g2.bx.psu.edu/view/iuc/vgp_split_agp/da61829dc3be)
+
+## FASTA/FASTQ
+
+- bbtools_bbduk was updated to [428de92eac6b](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbduk/428de92eac6b)
+- bbtools_bbmerge was updated to [f8734e69f645](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmerge/f8734e69f645)
+- bbtools_bbnorm was updated to [c80190b3ff02](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbnorm/c80190b3ff02)
+- bbtools_tadpole was updated to [8deeb4c5448b](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_tadpole/8deeb4c5448b)
+- poretools_events was updated to [daf8518d243a](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_events/daf8518d243a)
+- poretools_extract was updated to [08064da7b7fb](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_extract/08064da7b7fb)
+- poretools_hist was updated to [d1805f9c4c82](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_hist/d1805f9c4c82)
+- poretools_nucdist was updated to [5c4fa65f5733](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_nucdist/5c4fa65f5733)
+- poretools_occupancy was updated to [0433aad600e9](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_occupancy/0433aad600e9)
+- poretools_qualdist was updated to [72dfdbfab3cc](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_qualdist/72dfdbfab3cc)
+- poretools_qualpos was updated to [626b6c2be5c2](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_qualpos/626b6c2be5c2)
+- poretools_squiggle was updated to [26e6c9362b7b](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_squiggle/26e6c9362b7b)
+- poretools_stats was updated to [c1cbe2575d32](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_stats/c1cbe2575d32)
+- poretools_tabular was updated to [5f5f1da94d7f](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_tabular/5f5f1da94d7f)
+- poretools_times was updated to [107124859931](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_times/107124859931)
+- poretools_winner was updated to [6d93709247c7](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_winner/6d93709247c7)
+- poretools_yield_plot was updated to [c5c5a3e84989](https://toolshed.g2.bx.psu.edu/view/iuc/poretools_yield_plot/c5c5a3e84989)
+
+## Genome editing
+
+- mageck_count was updated to [e329d44424d7](https://toolshed.g2.bx.psu.edu/view/iuc/mageck_count/e329d44424d7)
+- mageck_gsea was updated to [b946929d31c4](https://toolshed.g2.bx.psu.edu/view/iuc/mageck_gsea/b946929d31c4)
+- mageck_mle was updated to [26126538a86f](https://toolshed.g2.bx.psu.edu/view/iuc/mageck_mle/26126538a86f)
+- mageck_pathway was updated to [39a996d44e16](https://toolshed.g2.bx.psu.edu/view/iuc/mageck_pathway/39a996d44e16)
+- mageck_test was updated to [9b4f4533c9ee](https://toolshed.g2.bx.psu.edu/view/iuc/mageck_test/9b4f4533c9ee)
+
+## Graph/Display Data
+
+- ggplot2_barplot was updated to [41e9114cc7cd](https://toolshed.g2.bx.psu.edu/view/iuc/ggplot2_barplot/41e9114cc7cd)
+- ggplot2_boxplot was updated to [653803fab921](https://toolshed.g2.bx.psu.edu/view/iuc/ggplot2_boxplot/653803fab921)
+- gwastools_manhattan_plot was updated to [c4bf5e913c2e](https://toolshed.g2.bx.psu.edu/view/iuc/gwastools_manhattan_plot/c4bf5e913c2e)
+- qq_manhattan was updated to [7a8a21c5a57f](https://toolshed.g2.bx.psu.edu/view/iuc/qq_manhattan/7a8a21c5a57f)
+
+## Mapping
+
+- bbtools_bbmap was updated to [23d04eabbac5](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmap/23d04eabbac5)
+- fastga was updated to [8f821f9b8567](https://toolshed.g2.bx.psu.edu/view/iuc/fastga/8f821f9b8567)
+- wfmash was updated to [45ff1e03f88a](https://toolshed.g2.bx.psu.edu/view/iuc/wfmash/45ff1e03f88a)
+
+## Phylogenetics
+
+- hyphy_b_still was updated to [0afe4b17fb2c](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_b_still/0afe4b17fb2c)
+- hyphy_cln was updated to [bf1ca3de3a76](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_cln/bf1ca3de3a76)
+- hyphy_infer_stasis_clusters was updated to [8a13bf04ca1f](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_infer_stasis_clusters/8a13bf04ca1f)
+
+## RNA Analysis
+
+- describe_samples was updated to [3b36efd62b3e](https://toolshed.g2.bx.psu.edu/view/iuc/describe_samples/3b36efd62b3e)
+- trinity_analyze_diff_expr was updated to [9ff3765e7172](https://toolshed.g2.bx.psu.edu/view/iuc/trinity_analyze_diff_expr/9ff3765e7172)
+- trinity_define_clusters_by_cutting_tree was updated to [65e7dea767ea](https://toolshed.g2.bx.psu.edu/view/iuc/trinity_define_clusters_by_cutting_tree/65e7dea767ea)
+- trinity_samples_qccheck was updated to [04bb8bb7c198](https://toolshed.g2.bx.psu.edu/view/iuc/trinity_samples_qccheck/04bb8bb7c198)
+
+## Text Manipulation
+
+- sqlite_to_tabular was updated to [c4d18aa4ec4a](https://toolshed.g2.bx.psu.edu/view/iuc/sqlite_to_tabular/c4d18aa4ec4a)
+
+## Variant Calling
+
+- bbtools_callvariants was updated to [68564cf83cb0](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_callvariants/68564cf83cb0)
+- bcftools_plugin_counts was updated to [ade0d3c3ec1c](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_counts/ade0d3c3ec1c)
+- bcftools_plugin_fill_an_ac was updated to [69ad30be1a8b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_an_ac/69ad30be1a8b)
+- bcftools_plugin_fill_tags was updated to [fea209b23f19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_tags/fea209b23f19)
+- bcftools_plugin_fixploidy was updated to [f203ea355bc8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fixploidy/f203ea355bc8)
+- bcftools_plugin_impute_info was updated to [42345cc2c76e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_impute_info/42345cc2c76e)
+- bcftools_plugin_missing2ref was updated to [793ae03deb13](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_missing2ref/793ae03deb13)
+- bcftools_query_list_samples was updated to [fb631fd605e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query_list_samples/fb631fd605e8)
+- gvcftools_extract_variants was updated to [bf8841b0a6b0](https://toolshed.g2.bx.psu.edu/view/iuc/gvcftools_extract_variants/bf8841b0a6b0)
+
+## None
+
+- data_manager_diamond_database_builder was updated to [4a08b7b76b78](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78)
+