On 2025-06-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #517

Text Manipulation

• text_processing was updated to c41d78ae5fee

Data and Metadata Management

• geo_cov_template was updated to 4f5816b57c13

Phylodiversity

• estimate_endem was updated to 7a952542e639

SAM/BAM

• sam_to_bam was updated to f7a0d41036c7

QIIME 2

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

ChemicalToolBox

• openbabel_compound_convert was updated to 1400d1977e7b
• gmx_merge_topology_files was updated to 04abdf96978b

Proteomics

• cardinal_mz_images was updated to 56b3b7d5f2b5
• hardklor was updated to 539f157784e7
• openms_epifany was updated to 03e13b23a78b
• openms_qccalculator was updated to 8bcc0d2ad96e

Assembly

• racon was updated to 936f0b5e7fcc
• metaspades was updated to 01a241476407

Graph/Display Data

• wordcloud was updated to 57e3de4b3b0d

Machine Learning

• sklearn_lightgbm was updated to 455ff9bec9b5
• sklearn_regression_metrics was updated to 70c5a9127f99

Metabolomics

• xcms_xcmsset was updated to 3bd53dcfa438

Imaging

• gate_finder was updated to db3053f1b878
• vitessce_spatial was updated to 70c8be4d59e9
• 2d_auto_threshold was updated to 50fa6150e340

Annotation

• omark was updated to 0291e0e81551
• ppanggolin_all was updated to 9e1870ae17e8
• ppanggolin_msa was updated to d82b7cc3dd30

Convert Formats

• tooldistillator was updated to dfd6fa2637ba
• tooldistillator_summarize was updated to 30a8447539e4
• ucsc_wigtobigwig was updated to 0dcdef015deb

FASTA/FASTQ

• fastq_groomer was updated to 71e5fa25b8a2
• fastp was updated to 480ddbd12a03
• ncbi_fcs_gx was updated to 04036a60676b
• cutadapt was updated to 80766b36005d

Gemini

• gemini_inheritance was updated to 162a9d4a3bdc
• gemini_query was updated to ab195e756e5e

Metagenomic Analysis

• dram_merge_annotations was updated to 96c0067106ec
• krakentools_alpha_diversity was updated to dc7fd9e2d835

Mothur

• mothur_cluster_split was updated to f73761825a11
• mothur_get_coremicrobiome was updated to 42244e3619cf
• mothur_pcr_seqs was updated to 482d26a40589

Phylogenetics

• hyphy_fade was updated to b959fd359a6b
• nextalign was updated to 41102a84e387

RNA Analysis

• cuffnorm was updated to f5b2ee725d34
• sleuth was updated to 2c3d294dbe42

Single-cell

• anndata_inspect was updated to 6a1a3dab235a

Variant Calling

• bcftools_call was updated to 3296c3680d96
• ensembl_vep was updated to 3a5a201f0bff
• smgu_frameshift_deletions_checks was updated to 81f337815c1b

None

• data_manager_diamond_database_builder was updated to 4a08b7b76b78
• data_manager_metaphlan_database_downloader was updated to 2c22b676ec46

hca_sc_scanpy_tools

• scanpy_plot_trajectory was updated to 8e2fc37c3e0c