feed.xml

<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.0.0">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>2025-02-03T02:47:22+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">UseGalaxy.eu Tool Updates for 2025-02-02</title><link href="https://galaxyproject.eu/posts/2025/02/02/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-02-02" /><published>2025-02-02T00:00:00+01:00</published><updated>2025-02-02T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/02/02/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/02/02/tool-update/">&lt;p&gt;On 2025-02-02, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#498/&quot;&gt;Jenkins Build #498&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ethevenot/heatmap/db1d80e89156&quot;&gt;db1d80e89156&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;dexseq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dexseq/74ec758e63a4&quot;&gt;74ec758e63a4&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;proteomics&quot;&gt;Proteomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fragpipe was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/fragpipe/048390db1932&quot;&gt;048390db1932&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;umi_tools_count was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/umi_tools_count/437d5c72f2e3&quot;&gt;437d5c72f2e3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;umi_tools_dedup was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/umi_tools_dedup/9cd1c2f5d90e&quot;&gt;9cd1c2f5d90e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;umi_tools_extract was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/umi_tools_extract/14ba4366aca4&quot;&gt;14ba4366aca4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;umi_tools_group was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/umi_tools_group/7f3b9b5db85c&quot;&gt;7f3b9b5db85c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;umi_tools_whitelist was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/umi_tools_whitelist/382326c1b1e1&quot;&gt;382326c1b1e1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;volcanoplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/volcanoplot/5e08a1e22dbc&quot;&gt;5e08a1e22dbc&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hicexplorer&quot;&gt;HiCExplorer&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hicexplorer_hicfindrestrictionsites was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/ad852622d00a&quot;&gt;ad852622d00a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_pre_cluster was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_pre_cluster/baba9fff9dba&quot;&gt;baba9fff9dba&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;multiple-alignments&quot;&gt;Multiple Alignments&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mummer_delta_filter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_delta_filter/2ab1e0e1c32e&quot;&gt;2ab1e0e1c32e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mummer_dnadiff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_dnadiff/4122b2fb7964&quot;&gt;4122b2fb7964&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mummer_mummer was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_mummer/2f4d9668d3b4&quot;&gt;2f4d9668d3b4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mummer_mummerplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_mummerplot/0c37cb9102d0&quot;&gt;0c37cb9102d0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mummer_nucmer was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_nucmer/fcad5e09a99d&quot;&gt;fcad5e09a99d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mummer_show_coords was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mummer_show_coords/e832875e5d5a&quot;&gt;e832875e5d5a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;send-data&quot;&gt;Send Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ena_upload was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/89329e428dc6&quot;&gt;89329e428dc6&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;single-cell&quot;&gt;Single-cell&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;spacexr_cside was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spacexr_cside/2b1797b4cbb1&quot;&gt;2b1797b4cbb1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;spacexr_rctd was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/spacexr_rctd/acf15b2efe66&quot;&gt;acf15b2efe66&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-02-02, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #498</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-01-27</title><link href="https://galaxyproject.eu/posts/2025/01/27/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-01-27" /><published>2025-01-27T00:00:00+01:00</published><updated>2025-01-27T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/01/27/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/01/27/tool-update/">&lt;p&gt;On 2025-01-27, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#497/&quot;&gt;Jenkins Build #497&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;quality-control&quot;&gt;Quality Control&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;multiqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/multiqc/a7e081ceb76a&quot;&gt;a7e081ceb76a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;proteomics&quot;&gt;Proteomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pyprophet_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/pyprophet_export/2bc6bbf651b9&quot;&gt;2bc6bbf651b9&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;imaging&quot;&gt;Imaging&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;binary2labelimage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/imgteam/binary2labelimage/6c92ac9ce868&quot;&gt;6c92ac9ce868&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;compleasm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/compleasm/7109a27a11db&quot;&gt;7109a27a11db&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;staramr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/staramr/6edfb4b6db85&quot;&gt;6edfb4b6db85&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/201eff2131d6&quot;&gt;201eff2131d6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_build_staramr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_staramr/3658cf4b6fd2&quot;&gt;3658cf4b6fd2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;emboss&quot;&gt;EMBOSS&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;emboss_needle was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/emboss_needle/2f0dc62d0a19&quot;&gt;2f0dc62d0a19&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;emboss_needleall was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/emboss_needleall/76373359fce2&quot;&gt;76373359fce2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;binette was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/binette/70b492856e17&quot;&gt;70b492856e17&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;metabat2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/metabat2/f375b4f6ef57&quot;&gt;f375b4f6ef57&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;metabat2_jgi_summarize_bam_contig_depths was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/metabat2_jgi_summarize_bam_contig_depths/00e3b4ef7e0c&quot;&gt;00e3b4ef7e0c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_add_rank_names was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_add_rank_names/2238658d7663&quot;&gt;2238658d7663&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/599a3fb9a953&quot;&gt;599a3fb9a953&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_dada2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/ae4d404a8227&quot;&gt;ae4d404a8227&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_bar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_bar/9302992205ad&quot;&gt;9302992205ad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_ordination was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/eab0b21652c4&quot;&gt;eab0b21652c4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_richness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/4faa9c663b38&quot;&gt;4faa9c663b38&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;phylogenetics&quot;&gt;Phylogenetics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;squirrel_phylo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/squirrel_phylo/b64098b87ea0&quot;&gt;b64098b87ea0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;squirrel_qc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/squirrel_qc/f63d24309f49&quot;&gt;f63d24309f49&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cnvkit_access was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_access/45805c2763d2&quot;&gt;45805c2763d2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_antitarget was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_antitarget/98a7ce7d42b8&quot;&gt;98a7ce7d42b8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_autobin was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_autobin/9940a098cfc8&quot;&gt;9940a098cfc8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_batch was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_batch/71f99b30a7f1&quot;&gt;71f99b30a7f1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_breaks was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_breaks/7a3b124bbe23&quot;&gt;7a3b124bbe23&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_call was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_call/519d405738ee&quot;&gt;519d405738ee&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_coverage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_coverage/9fd2e592743f&quot;&gt;9fd2e592743f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_diagram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_diagram/ce2ed9352a40&quot;&gt;ce2ed9352a40&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_bed was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_bed/9aeac47c89d1&quot;&gt;9aeac47c89d1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_cdt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_cdt/5406089c2db7&quot;&gt;5406089c2db7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_jtv was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_jtv/d30f7b4c0722&quot;&gt;d30f7b4c0722&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_nexus_basic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_nexus_basic/5f3e6356a8de&quot;&gt;5f3e6356a8de&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_nexus_ogt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_nexus_ogt/9ca92159a21a&quot;&gt;9ca92159a21a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_seg was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_seg/dbdb21b1d395&quot;&gt;dbdb21b1d395&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_export_vcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_export_vcf/d06c8938713a&quot;&gt;d06c8938713a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_fix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_fix/b02eb4c918f2&quot;&gt;b02eb4c918f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_genemetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_genemetrics/86662c490315&quot;&gt;86662c490315&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_heatmap/c76ce257611a&quot;&gt;c76ce257611a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_reference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_reference/ee80db1d39c0&quot;&gt;ee80db1d39c0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_scatter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_scatter/f96c79d645b6&quot;&gt;f96c79d645b6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segment was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segment/c576f0480c66&quot;&gt;c576f0480c66&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segmetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segmetrics/b28346e240f3&quot;&gt;b28346e240f3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_sex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_sex/94975590f584&quot;&gt;94975590f584&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_target was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_target/d14cfbdd41f0&quot;&gt;d14cfbdd41f0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_theta was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_theta/b10391f2e328&quot;&gt;b10391f2e328&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;snippy was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/snippy/08d22d220254&quot;&gt;08d22d220254&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;virology&quot;&gt;Virology&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;irma was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/irma/eddd9befb66d&quot;&gt;eddd9befb66d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_scanpy_tools&quot;&gt;hca_sc_scanpy_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;scanpy_read_10x was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_read_10x/72cf1c8f5870&quot;&gt;72cf1c8f5870&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_regress_variable was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_regress_variable/b8f8890d95e4&quot;&gt;b8f8890d95e4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_run_dpt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_dpt/ea6bea16d0e2&quot;&gt;ea6bea16d0e2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_run_fdg was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_run_fdg/425f2e046231&quot;&gt;425f2e046231&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;graphprot_predict_profile was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/rnateam/graphprot_predict_profile/4ad83aed5c3c&quot;&gt;4ad83aed5c3c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-01-27, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #497</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-01-19</title><link href="https://galaxyproject.eu/posts/2025/01/19/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-01-19" /><published>2025-01-19T00:00:00+01:00</published><updated>2025-01-19T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/01/19/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/01/19/tool-update/">&lt;p&gt;On 2025-01-19, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#496/&quot;&gt;Jenkins Build #496&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;data-and-metadata-management&quot;&gt;Data and Metadata Management&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;annotations_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/annotations_template/79f2ca0bfa9a&quot;&gt;79f2ca0bfa9a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eal_table_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eal_table_template/32707c9f5261&quot;&gt;32707c9f5261&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eal_table_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eal_table_template/8abb7c57a4b9&quot;&gt;8abb7c57a4b9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eal_templates was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eal_templates/3b0fa963ae3e&quot;&gt;3b0fa963ae3e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eal_templates was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eal_templates/404b7ff29b30&quot;&gt;404b7ff29b30&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eml2eal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eml2eal/0fa9d8240dc3&quot;&gt;0fa9d8240dc3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eml2eal was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eml2eal/57b8600443f5&quot;&gt;57b8600443f5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;eml_validate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/eml_validate/a652b7bc6322&quot;&gt;a652b7bc6322&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;entities_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/entities_template/1b11e38718af&quot;&gt;1b11e38718af&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;entities_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/entities_template/e24cfd8328c3&quot;&gt;e24cfd8328c3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;geo_cov_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/geo_cov_template/0fe3b8bd9d8b&quot;&gt;0fe3b8bd9d8b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;geo_cov_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/geo_cov_template/5c2ade73e411&quot;&gt;5c2ade73e411&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;makeeml was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/makeeml/34dcb86a9351&quot;&gt;34dcb86a9351&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;makeeml was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/makeeml/d6aa2a899877&quot;&gt;d6aa2a899877&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raster_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/raster_template/06e29cdc08bf&quot;&gt;06e29cdc08bf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raster_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/raster_template/eeadb27fe7b3&quot;&gt;eeadb27fe7b3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;taxo_cov_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/taxo_cov_template/20224597fa2c&quot;&gt;20224597fa2c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;taxo_cov_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/taxo_cov_template/293d3c8eba5c&quot;&gt;293d3c8eba5c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;vector_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/vector_template/330f15f2ad3f&quot;&gt;330f15f2ad3f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;vector_template was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/vector_template/67fbd4f439ed&quot;&gt;67fbd4f439ed&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;proteomics&quot;&gt;Proteomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;openms_xtandemadapter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xtandemadapter/1add9bacdccd&quot;&gt;1add9bacdccd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;tabpfn was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/tabpfn/c081e5e1d7ce&quot;&gt;c081e5e1d7ce&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;lotus2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/1d660ee0b1c8&quot;&gt;1d660ee0b1c8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;drep_compare was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/drep_compare/2c6f204ae1b9&quot;&gt;2c6f204ae1b9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;drep_dereplicate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/drep_dereplicate/76b57044069d&quot;&gt;76b57044069d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fairy_cov was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fairy_cov/f2fd2d1b96e3&quot;&gt;f2fd2d1b96e3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fairy_sketch was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fairy_sketch/008b08870cc0&quot;&gt;008b08870cc0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;braker3 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/genouest/braker3/a9b0b926e133&quot;&gt;a9b0b926e133&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-01-19, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #496</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-01-12</title><link href="https://galaxyproject.eu/posts/2025/01/12/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-01-12" /><published>2025-01-12T00:00:00+01:00</published><updated>2025-01-12T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/01/12/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/01/12/tool-update/">&lt;p&gt;On 2025-01-12, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#495/&quot;&gt;Jenkins Build #495&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_corr_axes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_corr_axes/0968daa9b52f&quot;&gt;0968daa9b52f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mothur_corr_axes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_corr_axes/0c76942a61e2&quot;&gt;0c76942a61e2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mothur_sens_spec was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_sens_spec/27171cf0b8ba&quot;&gt;27171cf0b8ba&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mothur_sffinfo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_sffinfo/09e3b0966a11&quot;&gt;09e3b0966a11&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;groot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/groot/4d5cf5a423d5&quot;&gt;4d5cf5a423d5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fastk_fastk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_fastk/34245579d255&quot;&gt;34245579d255&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fastk_histex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_histex/b897c5daf0ce&quot;&gt;b897c5daf0ce&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fastk_logex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_logex/73ddd200456a&quot;&gt;73ddd200456a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ggplot2_histogram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ggplot2_histogram/9d060114554c&quot;&gt;9d060114554c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;phyloseq_add_rank_names was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_add_rank_names/e51700388188&quot;&gt;e51700388188&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/b8a4de1a4e19&quot;&gt;b8a4de1a4e19&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/c0101c72b8af&quot;&gt;c0101c72b8af&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_dada2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/bda00cb136ee&quot;&gt;bda00cb136ee&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_bar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_bar/d0fa6a43c838&quot;&gt;d0fa6a43c838&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_ordination was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/f9543efabd85&quot;&gt;f9543efabd85&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_richness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/a20bc31f2821&quot;&gt;a20bc31f2821&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;single-cell&quot;&gt;Single-cell&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;anndata_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_export/83609ef746e9&quot;&gt;83609ef746e9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_import was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_import/13cf83ced60c&quot;&gt;13cf83ced60c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_inspect was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_inspect/33c0081e16c6&quot;&gt;33c0081e16c6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;anndata_manipulate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata_manipulate/d1e49c3c0aa2&quot;&gt;d1e49c3c0aa2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;modify_loom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/modify_loom/a7b951572609&quot;&gt;a7b951572609&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;scanpy_filter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_filter/5b3c1679d29b&quot;&gt;5b3c1679d29b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-01-12, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #495</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-01-05</title><link href="https://galaxyproject.eu/posts/2025/01/05/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-01-05" /><published>2025-01-05T00:00:00+01:00</published><updated>2025-01-05T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/01/05/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/01/05/tool-update/">&lt;p&gt;On 2025-01-05, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#494/&quot;&gt;Jenkins Build #494&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ectyper was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/ectyper/9cd096bee567&quot;&gt;9cd096bee567&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sklearn_clf_metrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sklearn_clf_metrics/55703205546f&quot;&gt;55703205546f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;chemicaltoolbox&quot;&gt;ChemicalToolBox&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gmx_editconf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_editconf/b9e25ec471eb&quot;&gt;b9e25ec471eb&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rad-seq&quot;&gt;RAD-seq&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;stacks_refmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/stacks_refmap/1ba1185929c1&quot;&gt;1ba1185929c1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_get_otulist was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_get_otulist/2478fb777d97&quot;&gt;2478fb777d97&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/9002633b4737&quot;&gt;9002633b4737&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_scanpy_tools&quot;&gt;hca_sc_scanpy_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;scanpy_plot_embed was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_plot_embed/210026a1a50a&quot;&gt;210026a1a50a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-01-05, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #494</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-29</title><link href="https://galaxyproject.eu/posts/2024/12/29/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-29" /><published>2024-12-29T00:00:00+01:00</published><updated>2024-12-29T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/29/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/29/tool-update/">&lt;p&gt;On 2024-12-29, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#493/&quot;&gt;Jenkins Build #493&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;chemicaltoolbox&quot;&gt;ChemicalToolBox&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gmx_solvate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_solvate/3c77d66e7fe5&quot;&gt;3c77d66e7fe5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;featurecounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/featurecounts/5dbff3a5845a&quot;&gt;5dbff3a5845a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphclust&quot;&gt;GraphClust&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;graphclust_postprocessing was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/rnateam/graphclust_postprocessing/e080ebe95476&quot;&gt;e080ebe95476&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pairtools_dedup was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pairtools_dedup/0bc216235d4c&quot;&gt;0bc216235d4c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pairtools_parse was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pairtools_parse/678f10bb377e&quot;&gt;678f10bb377e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pairtools_sort was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pairtools_sort/50d926b3f13d&quot;&gt;50d926b3f13d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pairtools_split was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pairtools_split/c46d1454f3a1&quot;&gt;c46d1454f3a1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pairtools_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pairtools_stats/7f71687c8146&quot;&gt;7f71687c8146&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gemini&quot;&gt;Gemini&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gemini_gene_wise was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gemini_gene_wise/4b26f6c99227&quot;&gt;4b26f6c99227&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/b6a38f6222af&quot;&gt;b6a38f6222af&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_dada2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/d1c93a32cb25&quot;&gt;d1c93a32cb25&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_bar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_bar/4ab2dbd11b21&quot;&gt;4ab2dbd11b21&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_ordination was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/5007bc8a3d90&quot;&gt;5007bc8a3d90&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_richness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/817853857084&quot;&gt;817853857084&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-29, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #493</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-22</title><link href="https://galaxyproject.eu/posts/2024/12/22/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-22" /><published>2024-12-22T00:00:00+01:00</published><updated>2024-12-22T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/22/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/22/tool-update/">&lt;p&gt;On 2024-12-22, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#492/&quot;&gt;Jenkins Build #492&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;augustus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/augustus/0fc0f9cf035a&quot;&gt;0fc0f9cf035a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;augustus_training was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/augustus_training/aada0deea587&quot;&gt;aada0deea587&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_build_icm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_build_icm/e903e26c014d&quot;&gt;e903e26c014d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_knowledge_based was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_knowledge_based/21d0af260f11&quot;&gt;21d0af260f11&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;glimmer_not_knowledge_based was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_not_knowledge_based/75cedbd8cf1b&quot;&gt;75cedbd8cf1b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;tetyper was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/tetyper/2b21643ce8d7&quot;&gt;2b21643ce8d7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ectyper was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/ectyper/daba54cd25ca&quot;&gt;daba54cd25ca&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sistr_cmd was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/sistr_cmd/cf767360ede1&quot;&gt;cf767360ede1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;compute-indicators-for-turnover-boulders-fields&quot;&gt;Compute indicators for turnover boulders fields&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cb_dissim was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/cb_dissim/ffaa9a71b2d2&quot;&gt;ffaa9a71b2d2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;phyloseq_plot_bar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_bar/ad81e112f4d9&quot;&gt;ad81e112f4d9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;staramr was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/nml/staramr/3548a93b39c1&quot;&gt;3548a93b39c1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;checkv_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/checkv_build_database/7e80c69020f7&quot;&gt;7e80c69020f7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;data-managers&quot;&gt;Data Managers&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;genomad_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/genomad_build_database/75abfb03b635&quot;&gt;75abfb03b635&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;vibrant_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/vibrant_build_database/e0faddfd9cf9&quot;&gt;e0faddfd9cf9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;virsorter_build_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/virsorter_build_database/c456ae8354f2&quot;&gt;c456ae8354f2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;glimmer_glimmer_to_gff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_glimmer_to_gff/3d71ab1562d7&quot;&gt;3d71ab1562d7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;jbrowse2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/21bb464c1d53&quot;&gt;21bb464c1d53&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metabolomics&quot;&gt;Metabolomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;xcms_xcmsset was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/lecorguille/xcms_xcmsset/3bd53dcfa438&quot;&gt;3bd53dcfa438&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/bc939965ce41&quot;&gt;bc939965ce41&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bcftools_csq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/33df4e68959b&quot;&gt;33df4e68959b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-22, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #492</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-15</title><link href="https://galaxyproject.eu/posts/2024/12/15/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-15" /><published>2024-12-15T00:00:00+01:00</published><updated>2024-12-15T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/15/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/15/tool-update/">&lt;p&gt;On 2024-12-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#491/&quot;&gt;Jenkins Build #491&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;graphdisplay-data&quot;&gt;Graph/Display Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;pygenometracks was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pygenometracks/59fd173ac850&quot;&gt;59fd173ac850&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;volcanoplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/volcanoplot/99ace6c1ff57&quot;&gt;99ace6c1ff57&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;proteomics&quot;&gt;Proteomics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fragpipe was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/fragpipe/e969a182e3cb&quot;&gt;e969a182e3cb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho/6140163233a5&quot;&gt;6140163233a5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho_grab_proteins was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho_grab_proteins/36dffb2bc194&quot;&gt;36dffb2bc194&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;proteinortho_summary was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho_summary/387d3633cade&quot;&gt;387d3633cade&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;get-data&quot;&gt;Get Data&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;uniprotxml_downloader was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/uniprotxml_downloader/4ddc8da62671&quot;&gt;4ddc8da62671&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gfastats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/gfastats/764f2516d837&quot;&gt;764f2516d837&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;text-manipulation&quot;&gt;Text Manipulation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;diff was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/diff/10ef1bf99074&quot;&gt;10ef1bf99074&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_build_kraken2_database was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/8c533e19b697&quot;&gt;8c533e19b697&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_ncbi_fcs_gx_database_downloader was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_ncbi_fcs_gx_database_downloader/6be6e6198ac3&quot;&gt;6be6e6198ac3&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decontam was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/decontam/3f238ab9d200&quot;&gt;3f238ab9d200&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mothur&quot;&gt;Mothur&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;mothur_get_lineage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_get_lineage/d1abc038d4bd&quot;&gt;d1abc038d4bd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;cnvkit_access was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_access/25bba7640b06&quot;&gt;25bba7640b06&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_antitarget was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_antitarget/dd54b5c36317&quot;&gt;dd54b5c36317&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_autobin was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_autobin/505e6bbaee59&quot;&gt;505e6bbaee59&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_batch was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_batch/97d2b6742760&quot;&gt;97d2b6742760&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_breaks was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_breaks/384fa596e5d9&quot;&gt;384fa596e5d9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_call was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_call/978ddcbedd60&quot;&gt;978ddcbedd60&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_coverage was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_coverage/5699301a3bd1&quot;&gt;5699301a3bd1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_diagram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_diagram/27ecb3477d34&quot;&gt;27ecb3477d34&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_fix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_fix/49ecf6b6f9f4&quot;&gt;49ecf6b6f9f4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_genemetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_genemetrics/3e1d74c9e715&quot;&gt;3e1d74c9e715&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_heatmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_heatmap/26554a14f841&quot;&gt;26554a14f841&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_reference was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_reference/b45fa373a972&quot;&gt;b45fa373a972&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_scatter was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_scatter/02446206f574&quot;&gt;02446206f574&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segment was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segment/33be231ce128&quot;&gt;33be231ce128&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_segmetrics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_segmetrics/86392285203a&quot;&gt;86392285203a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_sex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_sex/0b34f56003dc&quot;&gt;0b34f56003dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cnvkit_target was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cnvkit_target/428b93a3acb4&quot;&gt;428b93a3acb4&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #491</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-08</title><link href="https://galaxyproject.eu/posts/2024/12/08/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-08" /><published>2024-12-08T00:00:00+01:00</published><updated>2024-12-08T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/08/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/08/tool-update/">&lt;p&gt;On 2024-12-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#490/&quot;&gt;Jenkins Build #490&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;climate-analysis&quot;&gt;Climate Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;harmonize_insitu_to_netcdf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/harmonize_insitu_to_netcdf/15260949227d&quot;&gt;15260949227d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;mapping&quot;&gt;Mapping&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;rgrnastar was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rgrnastar/53255f6eecfc&quot;&gt;53255f6eecfc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;rna_starsolo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/rna_starsolo/381a32c51141&quot;&gt;381a32c51141&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;convert-formats&quot;&gt;Convert Formats&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;msconvert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert/ab6c14374bc0&quot;&gt;ab6c14374bc0&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;assembly&quot;&gt;Assembly&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;flye was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/flye/cd11366d92cf&quot;&gt;cd11366d92cf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fastk_fastk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastk_fastk/8049cb5537b7&quot;&gt;8049cb5537b7&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;machine-learning&quot;&gt;Machine Learning&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;black_forest_labs_flux was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/black_forest_labs_flux/7939ae8c5fd5&quot;&gt;7939ae8c5fd5&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;evolution&quot;&gt;Evolution&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;quicktree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/quicktree/1e89a460d1bd&quot;&gt;1e89a460d1bd&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hicexplorer&quot;&gt;HiCExplorer&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;hicexplorer_chicaggregatestatistic was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicaggregatestatistic/c3ffb2c1e314&quot;&gt;c3ffb2c1e314&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicdifferentialtest was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicdifferentialtest/45828071edc3&quot;&gt;45828071edc3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicexportdata was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicexportdata/1a31e75e979e&quot;&gt;1a31e75e979e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicplotviewpoint/920526260066&quot;&gt;920526260066&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicqualitycontrol was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicqualitycontrol/f6a169b5e43b&quot;&gt;f6a169b5e43b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicsignificantinteractions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicsignificantinteractions/ff1af7bac1cb&quot;&gt;ff1af7bac1cb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpoint/37125838e360&quot;&gt;37125838e360&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_chicviewpointbackgroundmodel was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpointbackgroundmodel/6f8debcf2ac9&quot;&gt;6f8debcf2ac9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicadjustmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicadjustmatrix/e8760fc0e29b&quot;&gt;e8760fc0e29b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaggregatecontacts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaggregatecontacts/30677e95bc89&quot;&gt;30677e95bc89&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaverageregions/3240e8a7c54f&quot;&gt;3240e8a7c54f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicbuildmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrix/d9967770de96&quot;&gt;d9967770de96&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccomparematrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccomparematrices/5dd1aae12f03&quot;&gt;5dd1aae12f03&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccompartmentspolarization was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccompartmentspolarization/87eb9c58cd19&quot;&gt;87eb9c58cd19&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicconvertformat was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicconvertformat/574f295b5ba4&quot;&gt;574f295b5ba4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrectmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrectmatrix/937b7b9832d0&quot;&gt;937b7b9832d0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hiccorrelate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrelate/0f5786ffa10d&quot;&gt;0f5786ffa10d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdetectloops/4375e25de06a&quot;&gt;4375e25de06a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicdifferentialtad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdifferentialtad/4977f65da0ff&quot;&gt;4977f65da0ff&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindrestrictionsites was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/f0b1bd38745a&quot;&gt;f0b1bd38745a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicfindtads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindtads/478aacfbaa37&quot;&gt;478aacfbaa37&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hichyperoptdetectloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hichyperoptdetectloops/3e5c86c2f80d&quot;&gt;3e5c86c2f80d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinfo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinfo/7fbd6feba1ca&quot;&gt;7fbd6feba1ca&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicinterintratad was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinterintratad/908fa330b93b&quot;&gt;908fa330b93b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergedomains was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergedomains/febfddb0b3e8&quot;&gt;febfddb0b3e8&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergeloops was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergeloops/1d9799f4b854&quot;&gt;1d9799f4b854&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicmergematrixbins was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergematrixbins/9d93c8fbe0a6&quot;&gt;9d93c8fbe0a6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicnormalize was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicnormalize/5e83c077e31d&quot;&gt;5e83c077e31d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicpca was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicpca/f86ca478c6af&quot;&gt;f86ca478c6af&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/3f1b286a5c34&quot;&gt;3f1b286a5c34&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotdistvscounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotdistvscounts/89cfe7de541b&quot;&gt;89cfe7de541b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotmatrix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotmatrix/025a128652dc&quot;&gt;025a128652dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotsvl was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotsvl/1602cc5b673c&quot;&gt;1602cc5b673c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicplotviewpoint was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotviewpoint/a10fce08c2dc&quot;&gt;a10fce08c2dc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicquickqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicquickqc/b13e7a200525&quot;&gt;b13e7a200525&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicsummatrices was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicsummatrices/d74cf4a61d65&quot;&gt;d74cf4a61d65&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hictransform was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hictransform/df64cc4dfb4d&quot;&gt;df64cc4dfb4d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;hicexplorer_hicvalidatelocations was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicvalidatelocations/d890828ab02a&quot;&gt;d890828ab02a&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;metagenomic-analysis&quot;&gt;Metagenomic Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;concoct_merge_cut_up_clustering was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/concoct_merge_cut_up_clustering/713189575b8b&quot;&gt;713189575b8b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_assigntaxonomyaddspecies was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_assigntaxonomyaddspecies/3a89c3f99f3d&quot;&gt;3a89c3f99f3d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_primercheck was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_primercheck/74ec28dbdf17&quot;&gt;74ec28dbdf17&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_removebimeradenovo was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_removebimeradenovo/1770d188f72d&quot;&gt;1770d188f72d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/1feea247d08a&quot;&gt;1feea247d08a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_from_dada2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/40ebae5bbe51&quot;&gt;40ebae5bbe51&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_ordination was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_ordination/c35e0075c7a2&quot;&gt;c35e0075c7a2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;phyloseq_plot_richness was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_plot_richness/1a6c2cc92c6e&quot;&gt;1a6c2cc92c6e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;ucsc_fatovcf was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_fatovcf/a40dd4fd3096&quot;&gt;a40dd4fd3096&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;data_manager_mapseq was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_mapseq/19ef193d1316&quot;&gt;19ef193d1316&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_scanpy_tools&quot;&gt;hca_sc_scanpy_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;scanpy_find_variable_genes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_find_variable_genes/d88a29e2eba6&quot;&gt;d88a29e2eba6&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-08, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #490</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2024-12-01</title><link href="https://galaxyproject.eu/posts/2024/12/01/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2024-12-01" /><published>2024-12-01T00:00:00+01:00</published><updated>2024-12-01T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2024/12/01/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2024/12/01/tool-update/">&lt;p&gt;On 2024-12-01, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#489/&quot;&gt;Jenkins Build #489&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;qiime-2&quot;&gt;QIIME 2&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2&quot;&gt;2572fc0f88f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;qiime2__deblur__denoise_16S was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623&quot;&gt;b883cbea5623&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gemini&quot;&gt;Gemini&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;gemini_fusions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gemini_fusions/8a68d9a33023&quot;&gt;8a68d9a33023&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;annotation&quot;&gt;Annotation&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;groot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/groot/c15e34e39e09&quot;&gt;c15e34e39e09&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;genome-diversity&quot;&gt;Genome Diversity&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;fasttree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fasttree/ef46a404db96&quot;&gt;ef46a404db96&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;rna-analysis&quot;&gt;RNA Analysis&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sfold was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sfold/6cce721f568c&quot;&gt;6cce721f568c&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;variant-calling&quot;&gt;Variant Calling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bcftools_consensus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/147de996e34f&quot;&gt;147de996e34f&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;none&quot;&gt;None&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;data_manager_diamond_database_builder was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78&quot;&gt;4a08b7b76b78&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;hca_sc_label_analysis_tools&quot;&gt;hca_sc_label_analysis_tools&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;decoupler_pseudobulk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/09c833d9b03b&quot;&gt;09c833d9b03b&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2024-12-01, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #489</summary></entry></feed>