On 2025-06-23, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #519

Data and Metadata Management

• taxo_cov_template was updated to 2af7401f13e0

Metabolomics

• ramclustr was updated to f52181a205d3
• ramclustr_define_experiment was updated to 7bbdcce50541
• ramclustr_define_experiment was updated to ef3cbcdf5f5d

QIIME 2

• qiime2__deblur__denoise_16S was updated to 2572fc0f88f2
• qiime2__deblur__denoise_16S was updated to b883cbea5623

ChemicalToolBox

• gmx_merge_topology_files was updated to 3c56532ba462

RNA Analysis

• cuffdiff was updated to d3ae7d9c2202
• deg_annotate was updated to e81fbbea6e8f

Gemini

• gemini_interactions was updated to 7028ca3cac1c

Proteomics

• openms_filemerger was updated to 8b871a67ba56
• proteinortho was updated to 16888c5c9ed5
• proteinortho_grab_proteins was updated to a83f63833669
• proteinortho_summary was updated to 8e27ee06aea4

Assembly

• minipolish was updated to bdfd7cef3438

Machine Learning

• sklearn_svm_classifier was updated to 7d7379dfef8b

Astronomy

• analyse_short_astro_text_astro_tool was updated to a35056104c2c
• desi_legacy_survey_astro_tool was updated to 7fad1abc2e4a

Annotation

• mirmachine was updated to b0d80d456120

Convert Formats

• samtools_bam_to_cram was updated to 85a38dffb93d

FASTA/FASTQ

• fastp was updated to e25816738ef3

Graph/Display Data

• ggplot2_point was updated to 9a482995958c

Metagenomic Analysis

• checkm_analyze was updated to f23a0598b4bc
• checkm_lineage_set was updated to a32ee0bb028b
• checkm_lineage_wf was updated to 482705438671
• checkm_plot was updated to 0ac2ba0b0d81
• checkm_qa was updated to 82caa8ed507c
• checkm_taxon_set was updated to 03c18e927a7e
• checkm_taxonomy_wf was updated to 0ea86ba426e1
• checkm_tetra was updated to 46bc08145439
• checkm_tree was updated to 626ab1058170
• checkm_tree_qa was updated to a99ca4bb4d1d

Mothur

• mothur_deunique_tree was updated to 1ace9d6863aa
• mothur_libshuff was updated to 1fe5098be27a
• mothur_summary_seqs was updated to 609770e516fa

NCBI Blast

• diamond was updated to 20d92dc4c6cb

Phylogenetics

• hyphy_meme was updated to 45a2366d777e
• squirrel_phylo was updated to 46a0e11a7607
• squirrel_qc was updated to d8d5380422c1

SAM/BAM

• bamtools was updated to 8eb649e67987
• bamtools_filter was updated to 62e4d6cdbaa7
• samtools_bedcov was updated to 762f63d4e25d
• samtools_calmd was updated to 3d5853a84711
• samtools_flagstat was updated to fbc6c28a5b14
• samtools_idxstats was updated to c9d9f721a568
• samtools_mpileup was updated to 32f6fffbc3e9
• samtools_reheader was updated to 2d7f0d455ad4
• samtools_slice_bam was updated to fea1a167b822
• samtools_sort was updated to 9ede25e390ff
• samtools_stats was updated to e221fe58c2f5
• samtools_ampliconclip was updated to f597cb9b33bf
• samtools_coverage was updated to ddbd49b892e5
• samtools_depth was updated to 772919943459
• samtools_fastx was updated to 9038311ed624
• samtools_fixmate was updated to c05afbeaf42d
• samtools_markdup was updated to 229ba92a3b55
• samtools_merge was updated to a7617eb92baf
• samtools_view was updated to 48bbbcb692ce

Text Manipulation

• table_compute was updated to cd36d6e45e29

Variant Calling

• freebayes was updated to 85dc96ebc770
• bcftools_convert_to_vcf was updated to fec517907949
• bcftools_csq was updated to 33df4e68959b

None

• data_manager_diamond_database_builder was updated to 4a08b7b76b78

hca_sc_scanpy_tools

• anndata_ops was updated to 7ef2403a250d

hca_sc_monocle3_tools

• monocle3_ordercells was updated to f58c4eb5446d

hca_sc_label_analysis_tools

• decoupler_pseudobulk was updated to 2557d7869e78

Single-cell

• quantification was updated to e11d5fafd0cc

Imaging

• scimap_anndata_to_csv was updated to 75bbd1b0e7bb