feed.xml

<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.4.1">Jekyll</generator><link href="https://galaxyproject.eu/feed.xml" rel="self" type="application/atom+xml" /><link href="https://galaxyproject.eu/" rel="alternate" type="text/html" /><updated>2026-10-26T02:45:59+01:00</updated><id>https://galaxyproject.eu/feed.xml</id><title type="html">Galaxy Europe</title><subtitle>The European Galaxy Instance</subtitle><entry><title type="html">Tool Update</title><link href="https://galaxyproject.eu/posts/2026/07/13/tool-update/" rel="alternate" type="text/html" title="Tool Update" /><published>2026-07-13T00:00:00+02:00</published><updated>2026-07-13T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/07/13/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/07/13/tool-update/"><![CDATA[]]></content><author><name></name></author><summary type="html"><![CDATA[]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-07-05</title><link href="https://galaxyproject.eu/posts/2026/07/05/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-07-05" /><published>2026-07-05T00:00:00+02:00</published><updated>2026-07-05T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/07/05/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/07/05/tool-update/"><![CDATA[<p>On 2026-07-05, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#597/">Jenkins Build #597</a></p>

<h2 id="population-genomics">Population Genomics</h2>

<ul>
  <li>effective_population_size_ld_method was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/effective_population_size_ld_method/44df6bc11647">44df6bc11647</a></li>
  <li>genetic_format_conversion was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/genetic_format_conversion/5969c92b20e4">5969c92b20e4</a></li>
  <li>population_genomics_split_vcf_by_pop was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/population_genomics_split_vcf_by_pop/82d7b529bd9e">82d7b529bd9e</a></li>
  <li>population_genomics_vcf_filtering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/population_genomics_vcf_filtering/53f9cb509272">53f9cb509272</a></li>
  <li>population_genomics_vcf_keep_remove_individuals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/population_genomics_vcf_keep_remove_individuals/c5227eed2880">c5227eed2880</a></li>
  <li>population_genomics_vcf_subset was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/population_genomics_vcf_subset/0b9504c6e514">0b9504c6e514</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="rna-analysis">RNA Analysis</h2>

<ul>
  <li>deseq2 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/deseq2/b060944b3989">b060944b3989</a></li>
  <li>eastr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/eastr/d2a78ce2b1f1">d2a78ce2b1f1</a></li>
  <li>tsenat was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/tsenat/2ead6d1194e6">2ead6d1194e6</a></li>
</ul>

<h2 id="convert-formats">Convert Formats</h2>

<ul>
  <li>msconvert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert/252d185267fc">252d185267fc</a></li>
  <li>geopandas_table2geojson was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/geopandas_table2geojson/4f831247b7ae">4f831247b7ae</a></li>
</ul>

<h2 id="assembly">Assembly</h2>

<ul>
  <li>instagraal was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/instagraal/5c11b91a76dc">5c11b91a76dc</a></li>
</ul>

<h2 id="graphdisplay-data">Graph/Display Data</h2>

<ul>
  <li>heatmap was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/heatmap/fe4ccc06e90e">fe4ccc06e90e</a></li>
</ul>

<h2 id="metagenomic-analysis">Metagenomic Analysis</h2>

<ul>
  <li>mags_visualization_comp_conta was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_comp_conta/50ac19944038">50ac19944038</a></li>
  <li>mags_visualization_drep_cluster_annot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_drep_cluster_annot/042531998360">042531998360</a></li>
  <li>mags_visualization_drep_cluster_func was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_drep_cluster_func/a70de587c7da">a70de587c7da</a></li>
  <li>mags_visualization_pathway_module_heatmap was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_pathway_module_heatmap/f729d5b6843a">f729d5b6843a</a></li>
  <li>mags_visualization_sample_heatmap was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_sample_heatmap/f9cd29b68158">f9cd29b68158</a></li>
  <li>mags_visualization_taxa_sankey was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mags_visualization_taxa_sankey/2e995d7dba20">2e995d7dba20</a></li>
</ul>

<h2 id="sambam">SAM/BAM</h2>

<ul>
  <li>samtools_faidx was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/samtools_faidx/78d6d62d4ce4">78d6d62d4ce4</a></li>
</ul>

<h2 id="single-cell">Single-cell</h2>

<ul>
  <li>sopa_aggregate was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/sopa_aggregate/57d6f5624178">57d6f5624178</a></li>
  <li>sopa_patchify was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/sopa_patchify/4aff1aa800d6">4aff1aa800d6</a></li>
  <li>sopa_report was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/sopa_report/5d9c0d2ab65f">5d9c0d2ab65f</a></li>
  <li>sopa_resolve was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/sopa_resolve/dce7456373c1">dce7456373c1</a></li>
  <li>sopa_segmentation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/sopa_segmentation/b640b0abe4c6">b640b0abe4c6</a></li>
</ul>

<h2 id="statistics">Statistics</h2>

<ul>
  <li>clustering_from_distmat was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/clustering_from_distmat/10abfe22d9c6">10abfe22d9c6</a></li>
  <li>general_matrix_tool was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/general_matrix_tool/b33018c9262e">b33018c9262e</a></li>
</ul>

<h2 id="variant-calling">Variant Calling</h2>

<ul>
  <li>ssiamb was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ssiamb/5a4d65354257">5a4d65354257</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>image_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/image_learner/7d84cdd45c15">7d84cdd45c15</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-07-05, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #597]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-28</title><link href="https://galaxyproject.eu/posts/2026/06/28/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-28" /><published>2026-06-28T00:00:00+02:00</published><updated>2026-06-28T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/28/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/28/tool-update/"><![CDATA[<p>On 2026-06-28, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#593/">Jenkins Build #593</a></p>

<h2 id="text-manipulation">Text Manipulation</h2>

<ul>
  <li>jq was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/jq/4e62e523c2b6">4e62e523c2b6</a></li>
</ul>

<h2 id="metabolomics">Metabolomics</h2>

<ul>
  <li>bioconductor_mzr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/bioconductor_mzr/27793114c209">27793114c209</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>image_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/image_learner/1d0a1899645e">1d0a1899645e</a></li>
  <li>image_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/image_learner/5a2a6da441ae">5a2a6da441ae</a></li>
  <li>aoptk_chemical_identifier was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_chemical_identifier/1453d8691711">1453d8691711</a></li>
  <li>aoptk_download_publication_data was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_download_publication_data/bb342034256d">bb342034256d</a></li>
  <li>aoptk_final_modification was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_final_modification/95fdcd130035">95fdcd130035</a></li>
  <li>aoptk_find_relationships_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_find_relationships_chemicals/35172fb694d8">35172fb694d8</a></li>
  <li>aoptk_normalize_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_normalize_chemicals/464344aefdec">464344aefdec</a></li>
  <li>aoptk_parse_pdf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_parse_pdf/bd64012e2ec3">bd64012e2ec3</a></li>
  <li>aoptk_publication_tracker was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_publication_tracker/98893ab7309f">98893ab7309f</a></li>
  <li>aoptk_publication_tracker was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_publication_tracker/d64165c2b96b">d64165c2b96b</a></li>
  <li>aoptk_query_literature was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_query_literature/7e6e180b1af7">7e6e180b1af7</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="gis-data-handling">GIS Data Handling</h2>

<ul>
  <li>3dtrees_standardization was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/3dtrees_standardization/e36c4b5d5cd9">e36c4b5d5cd9</a></li>
</ul>

<h2 id="annotation">Annotation</h2>

<ul>
  <li>dashing2_dist was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dashing2_dist/8ea4ecb79e95">8ea4ecb79e95</a></li>
  <li>dashing2_sketch was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dashing2_sketch/36c045dd663a">36c045dd663a</a></li>
  <li>dashing2_wsketch was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dashing2_wsketch/2b7561df23c0">2b7561df23c0</a></li>
  <li>rmlst_cli was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/rmlst_cli/c09eba7a47ee">c09eba7a47ee</a></li>
</ul>

<h2 id="astronomy">Astronomy</h2>

<ul>
  <li>gwtc_analysis was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/gwtc_analysis/d4336b333dac">d4336b333dac</a></li>
</ul>

<h2 id="get-data">Get Data</h2>

<ul>
  <li>ncbi_datasets was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_datasets/a7c1dc5207da">a7c1dc5207da</a></li>
</ul>

<h2 id="metagenomic-analysis">Metagenomic Analysis</h2>

<ul>
  <li>kaiju_addtaxonnames was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kaiju_addtaxonnames/4d2038a99775">4d2038a99775</a></li>
  <li>kaiju_kaiju was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kaiju_kaiju/72f3ef4a96e0">72f3ef4a96e0</a></li>
  <li>kaiju_kaiju2krona was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kaiju_kaiju2krona/b48d20647c74">b48d20647c74</a></li>
  <li>kaiju_kaiju2table was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kaiju_kaiju2table/3fe88629e18d">3fe88629e18d</a></li>
  <li>kaiju_mergeoutputs was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kaiju_mergeoutputs/72dc6be28a5f">72dc6be28a5f</a></li>
</ul>

<h2 id="ncbi-blast">NCBI Blast</h2>

<ul>
  <li>diamond was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/diamond/10fc1d5850a8">10fc1d5850a8</a></li>
</ul>

<h2 id="nanopore">Nanopore</h2>

<ul>
  <li>nanoplot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/nanoplot/3d8c0b287c51">3d8c0b287c51</a></li>
</ul>

<h2 id="single-cell">Single-cell</h2>

<ul>
  <li>liana_methods was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_methods/89635206a199">89635206a199</a></li>
  <li>liana_misty was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_misty/6466390eac09">6466390eac09</a></li>
  <li>liana_multi was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_multi/763dfad22665">763dfad22665</a></li>
  <li>liana_plot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_plot/1ffc708d7a5e">1ffc708d7a5e</a></li>
  <li>liana_resource was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_resource/ed517181d576">ed517181d576</a></li>
  <li>liana_utils was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/liana_utils/5bd0e9b7addf">5bd0e9b7addf</a></li>
  <li>raceid_clustering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/d2755d6016ca">d2755d6016ca</a></li>
  <li>raceid_filtnormconf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/b9712ed9c027">b9712ed9c027</a></li>
  <li>raceid_inspectclusters was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/22c726451b40">22c726451b40</a></li>
  <li>raceid_inspecttrajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/42a08854eb66">42a08854eb66</a></li>
  <li>raceid_trajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/2581f709c447">2581f709c447</a></li>
</ul>

<h2 id="variant-calling">Variant Calling</h2>

<ul>
  <li>vcfanno was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/vcfanno/2c526639f63c">2c526639f63c</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-28, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #593]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-23</title><link href="https://galaxyproject.eu/posts/2026/06/23/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-23" /><published>2026-06-23T00:00:00+02:00</published><updated>2026-06-23T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/23/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/23/tool-update/"><![CDATA[<p>On 2026-06-23, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#593/">Jenkins Build #593</a></p>

<h2 id="computer-vision">Computer Vision</h2>

<ul>
  <li>sam3_semantic_segmentation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/sam3_semantic_segmentation/e938172541c4">e938172541c4</a></li>
</ul>

<h2 id="chemicaltoolbox">ChemicalToolBox</h2>

<ul>
  <li>xtb_molecular_optimization was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/xtb_molecular_optimization/14a4d81e921e">14a4d81e921e</a></li>
</ul>

<h2 id="metabolomics">Metabolomics</h2>

<ul>
  <li>rcx_tk was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/rcx_tk/fd2837c28c34">fd2837c28c34</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>aoptk_chemical_identifier was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_chemical_identifier/0208d43952eb">0208d43952eb</a></li>
  <li>aoptk_download_publication_data was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_download_publication_data/792d078e6761">792d078e6761</a></li>
  <li>aoptk_download_publication_data was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_download_publication_data/c9c012f535f7">c9c012f535f7</a></li>
  <li>aoptk_final_modification was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_final_modification/53060147b091">53060147b091</a></li>
  <li>aoptk_final_modification was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_final_modification/fa78aa28937c">fa78aa28937c</a></li>
  <li>aoptk_find_relationships_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_find_relationships_chemicals/42c57f739aa1">42c57f739aa1</a></li>
  <li>aoptk_find_relationships_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_find_relationships_chemicals/7f92e08ad375">7f92e08ad375</a></li>
  <li>aoptk_normalize_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_normalize_chemicals/24b8c589e2eb">24b8c589e2eb</a></li>
  <li>aoptk_normalize_chemicals was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_normalize_chemicals/8180f16ac39c">8180f16ac39c</a></li>
  <li>aoptk_parse_pdf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_parse_pdf/0471403ef9ce">0471403ef9ce</a></li>
  <li>aoptk_parse_pdf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_parse_pdf/9a2ffe599e67">9a2ffe599e67</a></li>
  <li>aoptk_publication_tracker was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_publication_tracker/98893ab7309f">98893ab7309f</a></li>
  <li>aoptk_query_literature was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_query_literature/ecba3e952d53">ecba3e952d53</a></li>
  <li>aoptk_query_literature was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/aoptk_query_literature/efb219f82bb5">efb219f82bb5</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="annotation">Annotation</h2>

<ul>
  <li>amrfinderplus was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/amrfinderplus/96112e4c5e26">96112e4c5e26</a></li>
  <li>microsatbed was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/microsatbed/a3d1bf938fa8">a3d1bf938fa8</a></li>
</ul>

<h2 id="convert-formats">Convert Formats</h2>

<ul>
  <li>tooldistillator was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/tooldistillator/6c56786c9d1a">6c56786c9d1a</a></li>
  <li>tooldistillator_summarize was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/tooldistillator_summarize/95a71120949f">95a71120949f</a></li>
</ul>

<h2 id="metagenomic-analysis">Metagenomic Analysis</h2>

<ul>
  <li>dada2_assigntaxonomyaddspecies was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_assigntaxonomyaddspecies/60cd35f37c0a">60cd35f37c0a</a></li>
  <li>dada2_dada was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_dada/b762f4d54f78">b762f4d54f78</a></li>
  <li>dada2_filterandtrim was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_filterandtrim/6be249bfd55b">6be249bfd55b</a></li>
  <li>dada2_learnerrors was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_learnerrors/4bba91a89457">4bba91a89457</a></li>
  <li>dada2_makesequencetable was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_makesequencetable/aab8af79110e">aab8af79110e</a></li>
  <li>dada2_mergepairs was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_mergepairs/a35c40af067f">a35c40af067f</a></li>
  <li>dada2_plotcomplexity was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_plotcomplexity/5cba3a0dc3b6">5cba3a0dc3b6</a></li>
  <li>dada2_plotqualityprofile was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_plotqualityprofile/51971db051ba">51971db051ba</a></li>
  <li>dada2_primercheck was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_primercheck/506ce55ba922">506ce55ba922</a></li>
  <li>dada2_removebimeradenovo was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_removebimeradenovo/0a13d449d1bf">0a13d449d1bf</a></li>
  <li>dada2_seqcounts was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/dada2_seqcounts/256e7a119a95">256e7a119a95</a></li>
</ul>

<h2 id="single-cell">Single-cell</h2>

<ul>
  <li>raceid_clustering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/1c727d097441">1c727d097441</a></li>
  <li>raceid_filtnormconf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/bb9a4270e288">bb9a4270e288</a></li>
  <li>raceid_inspectclusters was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/25a519a368a4">25a519a368a4</a></li>
  <li>raceid_inspecttrajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/e5cd122b7555">e5cd122b7555</a></li>
  <li>raceid_trajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/8efd06e9899d">8efd06e9899d</a></li>
</ul>

<h2 id="variant-calling">Variant Calling</h2>

<ul>
  <li>fermi2 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/fermi2/2fba3825e828">2fba3825e828</a></li>
  <li>fermikit_variants was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/fermikit_variants/f05465a21e53">f05465a21e53</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-23, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #593]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-19</title><link href="https://galaxyproject.eu/posts/2026/06/19/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-19" /><published>2026-06-19T00:00:00+02:00</published><updated>2026-06-19T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/19/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/19/tool-update/"><![CDATA[<p>On 2026-06-19, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#591/">Jenkins Build #591</a></p>

<h2 id="gis-data-handling">GIS Data Handling</h2>

<ul>
  <li>aquainfra_ogc_api_processes was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/aquainfra_ogc_api_processes/cc99eeaa9a49">cc99eeaa9a49</a></li>
</ul>

<h2 id="population-genomics">Population Genomics</h2>

<ul>
  <li>dapc_kmeans was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/dapc_kmeans/4ca700803d75">4ca700803d75</a></li>
  <li>effective_population_size_ld_method was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/effective_population_size_ld_method/ecee96169b7c">ecee96169b7c</a></li>
  <li>lea_snmf_application was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/lea_snmf_application/8dadc1127183">8dadc1127183</a></li>
  <li>population_genetics_stats was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/population_genetics_stats/cd9b7f57a163">cd9b7f57a163</a></li>
</ul>

<h2 id="metabolomics">Metabolomics</h2>

<ul>
  <li>matchms_add_key was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_add_key/69b568a0dab1">69b568a0dab1</a></li>
  <li>matchms_convert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_convert/d95450eba471">d95450eba471</a></li>
  <li>matchms_filtering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_filtering/a26afcf352fd">a26afcf352fd</a></li>
  <li>matchms_fingerprint_similarity was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_fingerprint_similarity/a465cb84a388">a465cb84a388</a></li>
  <li>matchms_formatter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_formatter/5ab06f9104ec">5ab06f9104ec</a></li>
  <li>matchms_metadata_export was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_export/67b885502624">67b885502624</a></li>
  <li>matchms_metadata_match was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_match/9c9af0df1754">9c9af0df1754</a></li>
  <li>matchms_metadata_merge was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_metadata_merge/fda20b5ff8ed">fda20b5ff8ed</a></li>
  <li>matchms_networking was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_networking/ad859b8036ad">ad859b8036ad</a></li>
  <li>matchms_remove_key was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_key/9843a619e9be">9843a619e9be</a></li>
  <li>matchms_remove_spectra was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_remove_spectra/27e068d0d89a">27e068d0d89a</a></li>
  <li>matchms_spectral_similarity was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_spectral_similarity/931cce430163">931cce430163</a></li>
  <li>matchms_split was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_split/9e931f6fc8cd">9e931f6fc8cd</a></li>
  <li>matchms_subsetting was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/matchms_subsetting/0da72f66ff79">0da72f66ff79</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="assembly">Assembly</h2>

<ul>
  <li>mitohifi was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/mitohifi/2853471f753d">2853471f753d</a></li>
  <li>rnaspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/rnaspades/aa1ac2f7a688">aa1ac2f7a688</a></li>
  <li>spades_biosyntheticspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_biosyntheticspades/afac6d6bd02b">afac6d6bd02b</a></li>
  <li>spades_coronaspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_coronaspades/045c8498d2dd">045c8498d2dd</a></li>
  <li>spades_metaplasmidspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaplasmidspades/ae96f644b722">ae96f644b722</a></li>
  <li>spades_metaviralspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_metaviralspades/c4ba6aa27088">c4ba6aa27088</a></li>
  <li>spades_plasmidspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_plasmidspades/6fb81bb0fe3e">6fb81bb0fe3e</a></li>
  <li>spades_rnaviralspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/spades_rnaviralspades/f4fc734dd9b0">f4fc734dd9b0</a></li>
  <li>metaspades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/nml/metaspades/04d81e5f25e9">04d81e5f25e9</a></li>
  <li>spades was updated to <a href="https://toolshed.g2.bx.psu.edu/view/nml/spades/1f04936b96f3">1f04936b96f3</a></li>
</ul>

<h2 id="annotation">Annotation</h2>

<ul>
  <li>kat_cold was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/kat_cold/2ad6adc8d45f">2ad6adc8d45f</a></li>
  <li>kat_filter_kmer was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/kat_filter_kmer/6410f0530bc7">6410f0530bc7</a></li>
  <li>kat_filter_seq was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/kat_filter_seq/9dfc749e8eed">9dfc749e8eed</a></li>
  <li>kat_sect was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/kat_sect/bf55d2b3728c">bf55d2b3728c</a></li>
  <li>flavotyper was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/flavotyper/ef06acb676b4">ef06acb676b4</a></li>
  <li>mirmachine was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mirmachine/9c7074f01f52">9c7074f01f52</a></li>
  <li>staramr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/staramr/cfe8742b704e">cfe8742b704e</a></li>
  <li>tiberius was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/tiberius/0f10ac29126a">0f10ac29126a</a></li>
</ul>

<h2 id="graphdisplay-data">Graph/Display Data</h2>

<ul>
  <li>jbrowse2 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/dd032687675c">dd032687675c</a></li>
  <li>bandage was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/bandage/86ec2f06de3c">86ec2f06de3c</a></li>
</ul>

<h2 id="imaging">Imaging</h2>

<ul>
  <li>coco2labelme was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/coco2labelme/3a9709a4df77">3a9709a4df77</a></li>
  <li>coco_annotation_visualizer was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/coco_annotation_visualizer/7b390f574967">7b390f574967</a></li>
  <li>edit_coco_annotation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/edit_coco_annotation/b702f65d511e">b702f65d511e</a></li>
  <li>json2yolosegment was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/json2yolosegment/fe95917c3e20">fe95917c3e20</a></li>
  <li>yolo_predict was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/yolo_predict/3e9d14e5942f">3e9d14e5942f</a></li>
  <li>yolo_training was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/yolo_training/5cc588ef3793">5cc588ef3793</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>llm_hub was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/llm_hub/36d65981163b">36d65981163b</a></li>
  <li>image_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/image_learner/6b5934d4c7a9">6b5934d4c7a9</a></li>
  <li>multimodal_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/multimodal_learner/9649a6aa6997">9649a6aa6997</a></li>
  <li>tabular_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/tabular_learner/efe3a2d3a31d">efe3a2d3a31d</a></li>
</ul>

<h2 id="fastafastq">FASTA/FASTQ</h2>

<ul>
  <li>barcode_splitter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/barcode_splitter/eb95cc17426d">eb95cc17426d</a></li>
  <li>falco was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/falco/219ffa24f789">219ffa24f789</a></li>
</ul>

<h2 id="get-data">Get Data</h2>

<ul>
  <li>ncbi_datasets was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_datasets/c28c9cdf3660">c28c9cdf3660</a></li>
</ul>

<h2 id="mapping">Mapping</h2>

<ul>
  <li>bwa was updated to <a href="https://toolshed.g2.bx.psu.edu/view/devteam/bwa/c598cbb8b019">c598cbb8b019</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>amrfinderplus_data_manager_build was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/amrfinderplus_data_manager_build/5a6e1fa871a2">5a6e1fa871a2</a></li>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>

<h2 id="nanopore">Nanopore</h2>

<ul>
  <li>chopper was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/chopper/aa73f04777fd">aa73f04777fd</a></li>
</ul>

<h2 id="spatial-omics">Spatial Omics</h2>

<ul>
  <li>squidpy_graph was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/squidpy_graph/662e929f44fa">662e929f44fa</a></li>
  <li>squidpy_plot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/squidpy_plot/0a089e4b62d7">0a089e4b62d7</a></li>
</ul>

<h2 id="variant-calling">Variant Calling</h2>

<ul>
  <li>bcftools_norm was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/5226c31ac6d3">5226c31ac6d3</a></li>
  <li>ensembl_vep was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ensembl_vep/c8ecdd5bdb32">c8ecdd5bdb32</a></li>
</ul>

<h2 id="metagenomic-analysis">Metagenomic Analysis</h2>

<ul>
  <li>lotus2 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/869256447e86">869256447e86</a></li>
  <li>staramr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/nml/staramr/15a4fff208e4">15a4fff208e4</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-19, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #591]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-14</title><link href="https://galaxyproject.eu/posts/2026/06/14/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-14" /><published>2026-06-14T00:00:00+02:00</published><updated>2026-06-14T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/14/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/14/tool-update/"><![CDATA[<p>On 2026-06-14, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#591/">Jenkins Build #591</a></p>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-14, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #591]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-09</title><link href="https://galaxyproject.eu/posts/2026/06/09/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-09" /><published>2026-06-09T00:00:00+02:00</published><updated>2026-06-09T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/09/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/09/tool-update/"><![CDATA[<p>On 2026-06-09, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#590/">Jenkins Build #590</a></p>

<h2 id="dna-metabarcoding">DNA Metabarcoding</h2>

<ul>
  <li>obi_annotate was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_annotate/3ac96c352a3d">3ac96c352a3d</a></li>
  <li>obi_clean was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_clean/9c6619b29650">9c6619b29650</a></li>
  <li>obi_complement was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_complement/3eb53ac7fb0e">3eb53ac7fb0e</a></li>
  <li>obi_convert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_convert/618fa454e51a">618fa454e51a</a></li>
  <li>obi_grep was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_grep/e5cf6d670369">e5cf6d670369</a></li>
  <li>obi_multiplex was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_multiplex/a0169bbe7c7f">a0169bbe7c7f</a></li>
  <li>obi_pairing was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_pairing/9f6d6048be2c">9f6d6048be2c</a></li>
  <li>obi_pcr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_pcr/17bd2c9f1671">17bd2c9f1671</a></li>
  <li>obi_refidx was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_refidx/189cdb4ff7c2">189cdb4ff7c2</a></li>
  <li>obi_tag was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_tag/783ecd0c80fe">783ecd0c80fe</a></li>
  <li>obi_taxonomy was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_taxonomy/2073dc7c0c0c">2073dc7c0c0c</a></li>
  <li>obi_uniq was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_uniq/f2a8b93f731c">f2a8b93f731c</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="rna-analysis">RNA Analysis</h2>

<ul>
  <li>stringtie was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/stringtie/92198ab2345f">92198ab2345f</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>llm_hub was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/llm_hub/f5c7e6442a10">f5c7e6442a10</a></li>
</ul>

<h2 id="imaging">Imaging</h2>

<ul>
  <li>imagej2_adjust_threshold_binary was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_adjust_threshold_binary/1e1715e2b53d">1e1715e2b53d</a></li>
  <li>imagej2_analyze_particles_binary was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_analyze_particles_binary/0601a9056642">0601a9056642</a></li>
  <li>imagej2_analyze_skeleton was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_analyze_skeleton/3f5741e550e9">3f5741e550e9</a></li>
  <li>imagej2_binary_to_edm was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_binary_to_edm/4ae6e6b0258d">4ae6e6b0258d</a></li>
  <li>imagej2_bunwarpj_adapt_transform was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_adapt_transform/c853e60002db">c853e60002db</a></li>
  <li>imagej2_bunwarpj_align was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_align/a13240a1a6d3">a13240a1a6d3</a></li>
  <li>imagej2_bunwarpj_compare_elastic was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compare_elastic/c1c7a81ba4e5">c1c7a81ba4e5</a></li>
  <li>imagej2_bunwarpj_compare_elastic_raw was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compare_elastic_raw/07f37e516729">07f37e516729</a></li>
  <li>imagej2_bunwarpj_compare_raw was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compare_raw/2802f5bf9380">2802f5bf9380</a></li>
  <li>imagej2_bunwarpj_compose_elastic was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compose_elastic/71f2b1e4efa4">71f2b1e4efa4</a></li>
  <li>imagej2_bunwarpj_compose_raw was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compose_raw/231ca4c088d9">231ca4c088d9</a></li>
  <li>imagej2_bunwarpj_compose_raw_elastic was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_compose_raw_elastic/86886859d876">86886859d876</a></li>
  <li>imagej2_bunwarpj_convert_to_raw was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_convert_to_raw/c9e87324073c">c9e87324073c</a></li>
  <li>imagej2_bunwarpj_elastic_transform was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_elastic_transform/73b16a95813a">73b16a95813a</a></li>
  <li>imagej2_bunwarpj_raw_transform was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_bunwarpj_raw_transform/aed895206786">aed895206786</a></li>
  <li>imagej2_create_image was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_create_image/b63ed4bb2289">b63ed4bb2289</a></li>
  <li>imagej2_enhance_contrast was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_enhance_contrast/93cb13a320fe">93cb13a320fe</a></li>
  <li>imagej2_find_edges was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_find_edges/59b8bef26edf">59b8bef26edf</a></li>
  <li>imagej2_find_maxima was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_find_maxima/8bc0b21938d6">8bc0b21938d6</a></li>
  <li>imagej2_make_binary was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_make_binary/ac4aee7dc64c">ac4aee7dc64c</a></li>
  <li>imagej2_math was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_math/a2e5c70fdfcc">a2e5c70fdfcc</a></li>
  <li>imagej2_noise was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_noise/2b32aaa9a8b1">2b32aaa9a8b1</a></li>
  <li>imagej2_shadows was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_shadows/ec82bbbeb775">ec82bbbeb775</a></li>
  <li>imagej2_sharpen was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_sharpen/f4e396f032fc">f4e396f032fc</a></li>
  <li>imagej2_skeletonize3d was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_skeletonize3d/efbe484bc683">efbe484bc683</a></li>
  <li>imagej2_smooth was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_smooth/129f6b7185af">129f6b7185af</a></li>
  <li>imagej2_watershed_binary was updated to <a href="https://toolshed.g2.bx.psu.edu/view/imgteam/imagej2_watershed_binary/b92f57ebf6c8">b92f57ebf6c8</a></li>
</ul>

<h2 id="annotation">Annotation</h2>

<ul>
  <li>panaroo was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxy-australia/panaroo/3dc21aa05ec3">3dc21aa05ec3</a></li>
</ul>

<h2 id="fastafastq">FASTA/FASTQ</h2>

<ul>
  <li>art was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/art/b120e39b9f58">b120e39b9f58</a></li>
  <li>falco was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/falco/46192706f470">46192706f470</a></li>
</ul>

<h2 id="phylogenetics">Phylogenetics</h2>

<ul>
  <li>raxml was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raxml/0811b19b117a">0811b19b117a</a></li>
  <li>raxmlng was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raxmlng/1bc852b1d480">1bc852b1d480</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-09, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #590]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-07</title><link href="https://galaxyproject.eu/posts/2026/06/07/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-07" /><published>2026-06-07T00:00:00+02:00</published><updated>2026-06-07T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/07/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/07/tool-update/"><![CDATA[<p>On 2026-06-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#589/">Jenkins Build #589</a></p>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="rna-analysis">RNA Analysis</h2>

<ul>
  <li>recount3 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/recount3/3fed41a93e19">3fed41a93e19</a></li>
</ul>

<h2 id="text-manipulation">Text Manipulation</h2>

<ul>
  <li>nlp_cooccurrence_analysis was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/nlp_cooccurrence_analysis/740fdac23c32">740fdac23c32</a></li>
  <li>vader_sentiment was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/vader_sentiment/591d43098611">591d43098611</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-07, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #589]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-06-06</title><link href="https://galaxyproject.eu/posts/2026/06/06/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-06-06" /><published>2026-06-06T00:00:00+02:00</published><updated>2026-06-06T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/06/06/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/06/06/tool-update/"><![CDATA[<p>On 2026-06-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#587/">Jenkins Build #587</a></p>

<h2 id="quality-control">Quality Control</h2>

<ul>
  <li>multiqc was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/multiqc/fac2260bc88a">fac2260bc88a</a></li>
</ul>

<h2 id="dna-metabarcoding">DNA Metabarcoding</h2>

<ul>
  <li>obi_annotate was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_annotate/4da9a24971bd">4da9a24971bd</a></li>
  <li>obi_clean was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_clean/1beb31209adb">1beb31209adb</a></li>
  <li>obi_complement was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_complement/55d01781ffea">55d01781ffea</a></li>
  <li>obi_convert was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_convert/a86cb55cba33">a86cb55cba33</a></li>
  <li>obi_grep was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_grep/7e68109625a3">7e68109625a3</a></li>
  <li>obi_multiplex was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_multiplex/569eacd3be7b">569eacd3be7b</a></li>
  <li>obi_pairing was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_pairing/78598ed1b8a8">78598ed1b8a8</a></li>
  <li>obi_pcr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_pcr/a72c4cc8a704">a72c4cc8a704</a></li>
  <li>obi_refidx was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_refidx/61f9122bb420">61f9122bb420</a></li>
  <li>obi_tag was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_tag/fa01b4b07289">fa01b4b07289</a></li>
  <li>obi_taxonomy was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_taxonomy/9eb7ba86e367">9eb7ba86e367</a></li>
  <li>obi_uniq was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/obi_uniq/3cd66db293f6">3cd66db293f6</a></li>
</ul>

<h2 id="computer-vision">Computer Vision</h2>

<ul>
  <li>sam3_semantic_segmentation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/sam3_semantic_segmentation/9777101cccbc">9777101cccbc</a></li>
</ul>

<h2 id="population-genomics">Population Genomics</h2>

<ul>
  <li>effective_population_size_ld_method was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/effective_population_size_ld_method/2becf5e2f302">2becf5e2f302</a></li>
  <li>genetic_format_conversion was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/genetic_format_conversion/51eca2deef4e">51eca2deef4e</a></li>
  <li>ssrfilter was updated to <a href="https://toolshed.g2.bx.psu.edu/view/ecology/ssrfilter/67085b00bde1">67085b00bde1</a></li>
</ul>

<h2 id="metabolomics">Metabolomics</h2>

<ul>
  <li>isolib was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/isolib/a0a6127a7a69">a0a6127a7a69</a></li>
  <li>target_screen was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/target_screen/51f06fbad665">51f06fbad665</a></li>
  <li>use_theoretical_mz_annotations was updated to <a href="https://toolshed.g2.bx.psu.edu/view/recetox/use_theoretical_mz_annotations/ddd192ac60fe">ddd192ac60fe</a></li>
</ul>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="rna-analysis">RNA Analysis</h2>

<ul>
  <li>featurecounts was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/featurecounts/37d067694d40">37d067694d40</a></li>
  <li>tsenat was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/tsenat/efbf859ddd70">efbf859ddd70</a></li>
</ul>

<h2 id="proteomics">Proteomics</h2>

<ul>
  <li>maxquant was updated to <a href="https://toolshed.g2.bx.psu.edu/view/galaxyp/maxquant/fce1301d386c">fce1301d386c</a></li>
  <li>swissmodel_modelling_api was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/swissmodel_modelling_api/42fdfcbc63ea">42fdfcbc63ea</a></li>
</ul>

<h2 id="machine-learning">Machine Learning</h2>

<ul>
  <li>llm_hub was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/llm_hub/914dcb4df04c">914dcb4df04c</a></li>
  <li>image_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/image_learner/1d0a1899645e">1d0a1899645e</a></li>
  <li>multimodal_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/multimodal_learner/73af7d202e2a">73af7d202e2a</a></li>
  <li>tabular_learner was updated to <a href="https://toolshed.g2.bx.psu.edu/view/goeckslab/tabular_learner/575cb355247c">575cb355247c</a></li>
</ul>

<h2 id="other-tools">Other Tools</h2>

<ul>
  <li>3dtrees_metadata was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/3dtrees_metadata/d3cff3f1ff4e">d3cff3f1ff4e</a></li>
</ul>

<h2 id="annotation">Annotation</h2>

<ul>
  <li>prokka was updated to <a href="https://toolshed.g2.bx.psu.edu/view/crs4/prokka/c105b66eaab1">c105b66eaab1</a></li>
  <li>abritamr was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/abritamr/ce54031c2235">ce54031c2235</a></li>
  <li>drhip was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/drhip/e301c523e83d">e301c523e83d</a></li>
</ul>

<h2 id="convert-formats">Convert Formats</h2>

<ul>
  <li>ucsc_axtchain was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_axtchain/ac3a3feb4cf1">ac3a3feb4cf1</a></li>
</ul>

<h2 id="evolution">Evolution</h2>

<ul>
  <li>quicktree was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/quicktree/8ea036ce2f13">8ea036ce2f13</a></li>
</ul>

<h2 id="filter-and-sort">Filter and Sort</h2>

<ul>
  <li>bigwig_outlier_bed was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/bigwig_outlier_bed/57467b5debe6">57467b5debe6</a></li>
</ul>

<h2 id="get-data">Get Data</h2>

<ul>
  <li>ncbi_datasets was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_datasets/07f675a7ac2e">07f675a7ac2e</a></li>
</ul>

<h2 id="graphdisplay-data">Graph/Display Data</h2>

<ul>
  <li>seaborn was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/seaborn/c7cb57d16237">c7cb57d16237</a></li>
  <li>seaborn_pairgrid was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/seaborn_pairgrid/36f4aa9439a8">36f4aa9439a8</a></li>
  <li>upsetplot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/upsetplot/fa2e7ae6cad6">fa2e7ae6cad6</a></li>
</ul>

<h2 id="hicexplorer">HiCExplorer</h2>

<ul>
  <li>hicexplorer_chicaggregatestatistic was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicaggregatestatistic/65fc9fc648f4">65fc9fc648f4</a></li>
  <li>hicexplorer_chicdifferentialtest was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicdifferentialtest/7157e98ec11a">7157e98ec11a</a></li>
  <li>hicexplorer_chicexportdata was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicexportdata/0671a38a29d5">0671a38a29d5</a></li>
  <li>hicexplorer_chicplotviewpoint was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicplotviewpoint/009ea872cdf5">009ea872cdf5</a></li>
  <li>hicexplorer_chicqualitycontrol was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicqualitycontrol/853c072bbb11">853c072bbb11</a></li>
  <li>hicexplorer_chicsignificantinteractions was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicsignificantinteractions/e9cf8387e386">e9cf8387e386</a></li>
  <li>hicexplorer_chicviewpoint was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpoint/90d52ca89318">90d52ca89318</a></li>
  <li>hicexplorer_chicviewpointbackgroundmodel was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpointbackgroundmodel/fdb67db6d500">fdb67db6d500</a></li>
  <li>hicexplorer_hicadjustmatrix was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicadjustmatrix/733162fae8b0">733162fae8b0</a></li>
  <li>hicexplorer_hicaggregatecontacts was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaggregatecontacts/9c004f11ebe4">9c004f11ebe4</a></li>
  <li>hicexplorer_hicaverageregions was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaverageregions/0ec8d77d1833">0ec8d77d1833</a></li>
  <li>hicexplorer_hicbuildmatrix was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrix/453619f40b89">453619f40b89</a></li>
  <li>hicexplorer_hicbuildmatrixmicroc was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrixmicroc/d50fb8ae7e11">d50fb8ae7e11</a></li>
  <li>hicexplorer_hiccomparematrices was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccomparematrices/6f078762ff7f">6f078762ff7f</a></li>
  <li>hicexplorer_hiccompartmentspolarization was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccompartmentspolarization/4630448a0d88">4630448a0d88</a></li>
  <li>hicexplorer_hicconvertformat was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicconvertformat/0d0c6092cc43">0d0c6092cc43</a></li>
  <li>hicexplorer_hiccorrectmatrix was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrectmatrix/c5ce0cbf73dc">c5ce0cbf73dc</a></li>
  <li>hicexplorer_hiccorrelate was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrelate/5faa9d3839d0">5faa9d3839d0</a></li>
  <li>hicexplorer_hicdetectloops was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdetectloops/18bf75bf5d67">18bf75bf5d67</a></li>
  <li>hicexplorer_hicdifferentialtad was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdifferentialtad/5b245b3ded3f">5b245b3ded3f</a></li>
  <li>hicexplorer_hicfindrestrictionsites was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/430acc59e883">430acc59e883</a></li>
  <li>hicexplorer_hicfindtads was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindtads/7b9fa42ca59c">7b9fa42ca59c</a></li>
  <li>hicexplorer_hichyperoptdetectloops was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hichyperoptdetectloops/1fa29fabe773">1fa29fabe773</a></li>
  <li>hicexplorer_hicinfo was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinfo/58293f858e2d">58293f858e2d</a></li>
  <li>hicexplorer_hicinterintratad was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinterintratad/eddb1f249f6c">eddb1f249f6c</a></li>
  <li>hicexplorer_hicmergedomains was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergedomains/ee33791e32dc">ee33791e32dc</a></li>
  <li>hicexplorer_hicmergeloops was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergeloops/7f88b2b4662d">7f88b2b4662d</a></li>
  <li>hicexplorer_hicmergematrixbins was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergematrixbins/7011782fdbaf">7011782fdbaf</a></li>
  <li>hicexplorer_hicnormalize was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicnormalize/b1815cb2b298">b1815cb2b298</a></li>
  <li>hicexplorer_hicpca was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicpca/b03f8b95b08c">b03f8b95b08c</a></li>
  <li>hicexplorer_hicplotaverageregions was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/16a8d1688c65">16a8d1688c65</a></li>
  <li>hicexplorer_hicplotdistvscounts was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotdistvscounts/9f0578013f9b">9f0578013f9b</a></li>
  <li>hicexplorer_hicplotmatrix was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotmatrix/eb3a1b9a1c3c">eb3a1b9a1c3c</a></li>
  <li>hicexplorer_hicplotsvl was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotsvl/ff9f5d335041">ff9f5d335041</a></li>
  <li>hicexplorer_hicplotviewpoint was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotviewpoint/bb9e080ae77b">bb9e080ae77b</a></li>
  <li>hicexplorer_hicquickqc was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicquickqc/0a134c0bdb39">0a134c0bdb39</a></li>
  <li>hicexplorer_hicsummatrices was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicsummatrices/86958f9bec1b">86958f9bec1b</a></li>
  <li>hicexplorer_hictransform was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hictransform/a4b4bb07ed14">a4b4bb07ed14</a></li>
  <li>hicexplorer_hicvalidatelocations was updated to <a href="https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicvalidatelocations/4060d361cf3c">4060d361cf3c</a></li>
</ul>

<h2 id="mapping">Mapping</h2>

<ul>
  <li>kma was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/kma/6fe0fdd63a67">6fe0fdd63a67</a></li>
  <li>minimap2 was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/minimap2/f5b1e7d2594f">f5b1e7d2594f</a></li>
</ul>

<h2 id="metagenomic-analysis">Metagenomic Analysis</h2>

<ul>
  <li>mgnify_pipelines_toolkit_classify_var_regions was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_classify_var_regions/f50b54b40d7f">f50b54b40d7f</a></li>
  <li>mgnify_pipelines_toolkit_make_asv_count_table was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_make_asv_count_table/06f46257fea7">06f46257fea7</a></li>
  <li>mgnify_pipelines_toolkit_mapseq_to_asv_table was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_mapseq_to_asv_table/d7a50f1dae96">d7a50f1dae96</a></li>
  <li>mgnify_pipelines_toolkit_permute_primers was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_permute_primers/df3562628eb7">df3562628eb7</a></li>
  <li>mgnify_pipelines_toolkit_primer_val_classification was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_primer_val_classification/989443308ec9">989443308ec9</a></li>
  <li>mgnify_pipelines_toolkit_rev_comp_se_primers was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/mgnify_pipelines_toolkit_rev_comp_se_primers/56abee7b6395">56abee7b6395</a></li>
</ul>

<h2 id="nanopore">Nanopore</h2>

<ul>
  <li>nanoplot was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/nanoplot/640e4eeab4e2">640e4eeab4e2</a></li>
</ul>

<h2 id="phylogenetics">Phylogenetics</h2>

<ul>
  <li>blast_parser was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/blast_parser/f10c4abc0ab3">f10c4abc0ab3</a></li>
  <li>gafa was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/gafa/38b0685e442a">38b0685e442a</a></li>
  <li>gstf_preparation was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/gstf_preparation/8cff16cf17a8">8cff16cf17a8</a></li>
  <li>hcluster_sg was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg/e2a69a5aeb7e">e2a69a5aeb7e</a></li>
  <li>hcluster_sg_parser was updated to <a href="https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg_parser/6f9566d5a509">6f9566d5a509</a></li>
  <li>raxml was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raxml/dc97e1b45938">dc97e1b45938</a></li>
</ul>

<h2 id="single-cell">Single-cell</h2>

<ul>
  <li>anndata2ri was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/anndata2ri/3421d2ea2c8a">3421d2ea2c8a</a></li>
  <li>raceid_clustering was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/14ac9a11465e">14ac9a11465e</a></li>
  <li>raceid_filtnormconf was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/4d69676e6af2">4d69676e6af2</a></li>
  <li>raceid_inspectclusters was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/53d889b0a2c9">53d889b0a2c9</a></li>
  <li>raceid_inspecttrajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/9606d2385547">9606d2385547</a></li>
  <li>raceid_trajectory was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/fe9bf1aa669e">fe9bf1aa669e</a></li>
</ul>

<h2 id="variant-calling">Variant Calling</h2>

<ul>
  <li>artic_guppyplex was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/artic_guppyplex/e92767bd4412">e92767bd4412</a></li>
  <li>artic_minion was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/artic_minion/c218cc6bf765">c218cc6bf765</a></li>
  <li>plink was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/plink/9c48485bf664">9c48485bf664</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-06-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #587]]></summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2026-05-31</title><link href="https://galaxyproject.eu/posts/2026/05/31/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2026-05-31" /><published>2026-05-31T00:00:00+02:00</published><updated>2026-05-31T00:00:00+02:00</updated><id>https://galaxyproject.eu/posts/2026/05/31/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2026/05/31/tool-update/"><![CDATA[<p>On 2026-05-31, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in <a href="https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#586/">Jenkins Build #586</a></p>

<h2 id="qiime-2">QIIME 2</h2>

<ul>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2">2572fc0f88f2</a></li>
  <li>qiime2__deblur__denoise_16S was updated to <a href="https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623">b883cbea5623</a></li>
</ul>

<h2 id="none">None</h2>

<ul>
  <li>data_manager_diamond_database_builder was updated to <a href="https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78">4a08b7b76b78</a></li>
</ul>]]></content><author><name></name></author><category term="tools" /><summary type="html"><![CDATA[On 2026-05-31, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #586]]></summary></entry></feed>