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>2025-02-21T02:47:47+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 2025-02-20</title><link href="https://galaxyproject.eu/posts/2025/02/20/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-02-20" /><published>2025-02-20T00:00:00+01:00</published><updated>2025-02-20T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/02/20/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/02/20/tool-update/">&lt;p&gt;On 2025-02-20, 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/#501/&quot;&gt;Jenkins Build #501&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/31c42a2c02d3&quot;&gt;31c42a2c02d3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;multiqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/multiqc/d2aaac19f42f&quot;&gt;d2aaac19f42f&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;fastafastq&quot;&gt;FASTA/FASTQ&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;bbtools_bbduk was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbduk/55e500606bbe&quot;&gt;55e500606bbe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_bbmerge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmerge/08b2f8e6846d&quot;&gt;08b2f8e6846d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_bbnorm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbnorm/5f047a0d4c2e&quot;&gt;5f047a0d4c2e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_tadpole was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_tadpole/7ad0f4bfa923&quot;&gt;7ad0f4bfa923&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sickle was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/sickle/9108bd9450cb&quot;&gt;9108bd9450cb&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;cardinal_classification was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/galaxyp/cardinal_classification/42f6e30b00f2&quot;&gt;42f6e30b00f2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;sambam&quot;&gt;SAM/BAM&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;sambamba_flagstat was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sambamba_flagstat/cfd6e76541ff&quot;&gt;cfd6e76541ff&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sambamba_markdup was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sambamba_markdup/a348429b6fec&quot;&gt;a348429b6fec&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sambamba_merge was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sambamba_merge/66a7ee77d7e3&quot;&gt;66a7ee77d7e3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;sambamba_sort was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/sambamba_sort/6aa99e436263&quot;&gt;6aa99e436263&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/e7b4afedc471&quot;&gt;e7b4afedc471&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/7834132949bc&quot;&gt;7834132949bc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;biobox_add_taxid was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/biobox_add_taxid/7a9dd5efc076&quot;&gt;7a9dd5efc076&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/40d5ea45b73f&quot;&gt;40d5ea45b73f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/fac3911ad3b6&quot;&gt;fac3911ad3b6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;checkm2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/checkm2/0f5f7fa9c08f&quot;&gt;0f5f7fa9c08f&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/705d26fbea02&quot;&gt;705d26fbea02&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_dada was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_dada/b35a5e8ff0fe&quot;&gt;b35a5e8ff0fe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_filterandtrim was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_filterandtrim/00e0347751b1&quot;&gt;00e0347751b1&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_learnerrors was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_learnerrors/a14a18a47c36&quot;&gt;a14a18a47c36&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_makesequencetable was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_makesequencetable/ebd632e95aae&quot;&gt;ebd632e95aae&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_mergepairs was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_mergepairs/646c58820267&quot;&gt;646c58820267&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_plotcomplexity was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_plotcomplexity/6f06d501b7e6&quot;&gt;6f06d501b7e6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_plotqualityprofile was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_plotqualityprofile/4e469b758915&quot;&gt;4e469b758915&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/ee763baa80c3&quot;&gt;ee763baa80c3&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/efe26de231ec&quot;&gt;efe26de231ec&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;dada2_seqcounts was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/dada2_seqcounts/390bc2645138&quot;&gt;390bc2645138&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/d94e49509dac&quot;&gt;d94e49509dac&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/a8806f3d45bb&quot;&gt;a8806f3d45bb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;nonpareil was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/nonpareil/9016f67b716f&quot;&gt;9016f67b716f&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/33079540e88f&quot;&gt;33079540e88f&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/1fcb1a2950cb&quot;&gt;1fcb1a2950cb&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/3e5642ac5620&quot;&gt;3e5642ac5620&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/ec82f2b95e89&quot;&gt;ec82f2b95e89&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/fb6b6d5e6bd5&quot;&gt;fb6b6d5e6bd5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;megahit was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/megahit/ab208c87d973&quot;&gt;ab208c87d973&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;raven was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/raven/27a172326f4e&quot;&gt;27a172326f4e&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;cp_common was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/cp_common/0b7db679fff8&quot;&gt;0b7db679fff8&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;deeparg_predict was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/deeparg_predict/3953324f6d31&quot;&gt;3953324f6d31&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;deeparg_short_reads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/deeparg_short_reads/558018b49a4c&quot;&gt;558018b49a4c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ppanggolin_all was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ppanggolin_all/a83148dac159&quot;&gt;a83148dac159&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ppanggolin_msa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ppanggolin_msa/76170454dc91&quot;&gt;76170454dc91&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/9e8cf8dd6955&quot;&gt;9e8cf8dd6955&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_deeparg was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_deeparg/4a72de3780aa&quot;&gt;4a72de3780aa&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;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/5c2ac7f640ab&quot;&gt;5c2ac7f640ab&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_hicplotaverageregions was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/2371fad10021&quot;&gt;2371fad10021&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;bbtools_bbmap was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmap/20ab37575227&quot;&gt;20ab37575227&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;nanopore&quot;&gt;Nanopore&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;clair3 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/clair3/c9218b9dc7f0&quot;&gt;c9218b9dc7f0&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;medaka_consensus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/medaka_consensus/0413e62b757a&quot;&gt;0413e62b757a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;porechop was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/porechop/a2899db6bd6e&quot;&gt;a2899db6bd6e&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/eaa0b1e114eb&quot;&gt;eaa0b1e114eb&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/cd668d67431e&quot;&gt;cd668d67431e&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/440074098911&quot;&gt;440074098911&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;anndata2ri was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/anndata2ri/ac675f28acfc&quot;&gt;ac675f28acfc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cluster_analyze_embed_muon was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cluster_analyze_embed_muon/6c971179bb3f&quot;&gt;6c971179bb3f&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;mudata_import_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mudata_import_export/73a8649345f7&quot;&gt;73a8649345f7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;plot_muon was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/plot_muon/6446eb1889da&quot;&gt;6446eb1889da&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;preprocess_muon was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/preprocess_muon/bd31b5d2130a&quot;&gt;bd31b5d2130a&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;table_compute was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/table_compute/56a8da1f2243&quot;&gt;56a8da1f2243&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;bbtools_callvariants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_callvariants/b4279a293312&quot;&gt;b4279a293312&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;freyja_aggregate_plot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_aggregate_plot/640c0b8cc8bf&quot;&gt;640c0b8cc8bf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_boot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_boot/cd5d77d118f2&quot;&gt;cd5d77d118f2&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_demix was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_demix/e7a2086a0f03&quot;&gt;e7a2086a0f03&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;freyja_variants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/freyja_variants/11c062caec10&quot;&gt;11c062caec10&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ivar_consensus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ivar_consensus/196d126cd016&quot;&gt;196d126cd016&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ivar_filtervariants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ivar_filtervariants/d328d99d7396&quot;&gt;d328d99d7396&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ivar_removereads was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ivar_removereads/9f4805c61d29&quot;&gt;9f4805c61d29&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ivar_trim was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ivar_trim/c9ef01b1cfba&quot;&gt;c9ef01b1cfba&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ivar_variants was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ivar_variants/41c7ba073a9b&quot;&gt;41c7ba073a9b&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;ensembl_get_feature_info was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/earlhaminst/ensembl_get_feature_info/37cdb55f5258&quot;&gt;37cdb55f5258&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ensembl_get_genetree was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/earlhaminst/ensembl_get_genetree/935de83b470b&quot;&gt;935de83b470b&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ensembl_get_sequences was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/earlhaminst/ensembl_get_sequences/c79ce2342f1e&quot;&gt;c79ce2342f1e&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;</content><author><name></name></author><category term="tools" /><summary type="html">On 2025-02-20, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #501</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-02-16</title><link href="https://galaxyproject.eu/posts/2025/02/16/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-02-16" /><published>2025-02-16T00:00:00+01:00</published><updated>2025-02-16T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/02/16/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/02/16/tool-update/">&lt;p&gt;On 2025-02-16, 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/#500/&quot;&gt;Jenkins Build #500&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;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/8049cb5537b7&quot;&gt;8049cb5537b7&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;cami_amber was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber/e30bc6da7a36&quot;&gt;e30bc6da7a36&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_add was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_add/04f8949026bf&quot;&gt;04f8949026bf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/bc40aa3adf28&quot;&gt;bc40aa3adf28&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;kraken_biom was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/kraken_biom/65eb9962d272&quot;&gt;65eb9962d272&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_otus was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mothur_get_otus/976e1434503d&quot;&gt;976e1434503d&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;nanopore&quot;&gt;Nanopore&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;medaka_variant_pipeline was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/medaka_variant_pipeline/711d4deb7bdf&quot;&gt;711d4deb7bdf&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 2025-02-16, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #500</summary></entry><entry><title type="html">UseGalaxy.eu Tool Updates for 2025-02-09</title><link href="https://galaxyproject.eu/posts/2025/02/09/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2025-02-09" /><published>2025-02-09T00:00:00+01:00</published><updated>2025-02-09T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2025/02/09/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2025/02/09/tool-update/">&lt;p&gt;On 2025-02-09, 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/#499/&quot;&gt;Jenkins Build #499&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;histogram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/devteam/histogram/d0b9dd19e919&quot;&gt;d0b9dd19e919&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;gis-data-handling&quot;&gt;GIS Data Handling&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;aquainfra_ogc_api_processes was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ecology/aquainfra_ogc_api_processes/af00a67d3649&quot;&gt;af00a67d3649&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;bioconductor_scp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/bioconductor_scp/cd2f3a280463&quot;&gt;cd2f3a280463&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;gem_check_memote was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gem_check_memote/927af80d5e38&quot;&gt;927af80d5e38&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;gem_escher_visualization was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gem_escher_visualization/b79cf44068bc&quot;&gt;b79cf44068bc&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;gem_extract_exchange was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gem_extract_exchange/d9893d41dd6a&quot;&gt;d9893d41dd6a&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;gem_flux_distribution was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/gem_flux_distribution/1c71660496fb&quot;&gt;1c71660496fb&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bioconductor_msnbase_centroid was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/bioconductor_msnbase_centroid/4018639dc0a5&quot;&gt;4018639dc0a5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bioconductor_msnbase_smooth_chromatogram was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/bioconductor_msnbase_smooth_chromatogram/492350f45be9&quot;&gt;492350f45be9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bioconductor_msnbase_smooth_mz was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/bioconductor_msnbase_smooth_mz/00e058234fbf&quot;&gt;00e058234fbf&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;table_pandas_arithmetics was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/table_pandas_arithmetics/d4bacc06365e&quot;&gt;d4bacc06365e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;table_pandas_rename_column was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/table_pandas_rename_column/3f54cd56a65e&quot;&gt;3f54cd56a65e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;table_pandas_rename_columns_regex was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/table_pandas_rename_columns_regex/505a8e975968&quot;&gt;505a8e975968&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;table_pandas_transform was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/table_pandas_transform/b722dba91064&quot;&gt;b722dba91064&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;table_scipy_interpolate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/recetox/table_scipy_interpolate/0112f08c95ed&quot;&gt;0112f08c95ed&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;omero_get_id was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/omero_get_id/c7b2650718fe&quot;&gt;c7b2650718fe&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;omero_get_value was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/omero_get_value/ecb13e93fae2&quot;&gt;ecb13e93fae2&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;statistics&quot;&gt;Statistics&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;saqc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/saqc/55bbea0cdc60&quot;&gt;55bbea0cdc60&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;xlsx2tsv was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/ufz/xlsx2tsv/a21347be425d&quot;&gt;a21347be425d&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;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/7729cd89aaf7&quot;&gt;7729cd89aaf7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;bbtools_bbnorm was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbnorm/e607b61a68ad&quot;&gt;e607b61a68ad&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;fastp was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/fastp/10678d49d39e&quot;&gt;10678d49d39e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_fx2tab was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_fx2tab/13e101f5bb5d&quot;&gt;13e101f5bb5d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_head was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_head/3c0120a0e35c&quot;&gt;3c0120a0e35c&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_locate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_locate/54e818ea7c4d&quot;&gt;54e818ea7c4d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_sort was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_sort/3dc878f71e4d&quot;&gt;3dc878f71e4d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_stats was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_stats/70b975dca7b4&quot;&gt;70b975dca7b4&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;seqkit_translate was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_translate/f917a77055f5&quot;&gt;f917a77055f5&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cutadapt was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/c0b2c2e39c9c&quot;&gt;c0b2c2e39c9c&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;hicexplorer_hicbuildmatrixmicroc was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/hicexplorer_hicbuildmatrixmicroc/bce0ab313a89&quot;&gt;bce0ab313a89&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ppanggolin_all was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ppanggolin_all/6fdee3720de7&quot;&gt;6fdee3720de7&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;ppanggolin_msa was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ppanggolin_msa/d305623d5f41&quot;&gt;d305623d5f41&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;minimap2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/minimap2/66367287b4e6&quot;&gt;66367287b4e6&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;pbmm2 was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/pbmm2/4436bcb33d39&quot;&gt;4436bcb33d39&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/6641160f2053&quot;&gt;6641160f2053&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;biobox_add_taxid was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/biobox_add_taxid/2e0af1e2d487&quot;&gt;2e0af1e2d487&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber/319b8aac032d&quot;&gt;319b8aac032d&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_add was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_add/741babee7bb3&quot;&gt;741babee7bb3&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;cami_amber_convert was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/40d5ea45b73f&quot;&gt;40d5ea45b73f&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/8a9a425f5c60&quot;&gt;8a9a425f5c60&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/17d174efa4be&quot;&gt;17d174efa4be&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/d34e74e40d60&quot;&gt;d34e74e40d60&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/847f433f202b&quot;&gt;847f433f202b&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_dada2/0b9d4ec77c4f&quot;&gt;0b9d4ec77c4f&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/94563110275d&quot;&gt;94563110275d&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/bbd9d1022144&quot;&gt;bbd9d1022144&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/d6cbeb48294d&quot;&gt;d6cbeb48294d&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/5c7e6ef78006&quot;&gt;5c7e6ef78006&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/29662f643859&quot;&gt;29662f643859&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/b7bc272143fb&quot;&gt;b7bc272143fb&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/029a793f39b6&quot;&gt;029a793f39b6&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/27fff8d3793e&quot;&gt;27fff8d3793e&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/4c89814871e8&quot;&gt;4c89814871e8&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;ncbi-blast&quot;&gt;NCBI Blast&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;diamond was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/bgruening/diamond/60f307965815&quot;&gt;60f307965815&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h2 id=&quot;nanopore&quot;&gt;Nanopore&lt;/h2&gt;

&lt;ul&gt;
  &lt;li&gt;nanoplot was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/nanoplot/2a9afed42353&quot;&gt;2a9afed42353&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;ete_treeviewer was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/ete_treeviewer/2d4402c70eed&quot;&gt;2d4402c70eed&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;cemitool was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/cemitool/51a3b375b7b8&quot;&gt;51a3b375b7b8&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;mudata_import_export was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/mudata_import_export/089a6101d5d9&quot;&gt;089a6101d5d9&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;plot_muon was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/plot_muon/36f2cd69d20e&quot;&gt;36f2cd69d20e&lt;/a&gt;&lt;/li&gt;
  &lt;li&gt;preprocess_muon was updated to &lt;a href=&quot;https://toolshed.g2.bx.psu.edu/view/iuc/preprocess_muon/678260997e94&quot;&gt;678260997e94&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 2025-02-09, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #499</summary></entry><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></feed>