From e48ec360388b036f35aa875c3dc0ac990b8a42c2 Mon Sep 17 00:00:00 2001 From: "UseGalaxy.EU Jenkins Bot" Date: Sun, 24 Mar 2024 21:43:04 +0100 Subject: [PATCH] Autoupdate tool blog post --- _posts/2024-03-24-tool-update.md | 126 +++++++++++++++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 _posts/2024-03-24-tool-update.md diff --git a/_posts/2024-03-24-tool-update.md b/_posts/2024-03-24-tool-update.md new file mode 100644 index 000000000..4eca8c32c --- /dev/null +++ b/_posts/2024-03-24-tool-update.md @@ -0,0 +1,126 @@ +--- +site: freiburg +tags: [tools] +title: UseGalaxy.eu Tool Updates for 2024-03-24 +supporters: +- denbi +- elixir +--- + +On 2024-03-24, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #437](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#437/) + + +## DNA Metabarcoding + +- obi_annotate was updated to [d50dc96e3ce9](https://toolshed.g2.bx.psu.edu/view/iuc/obi_annotate/d50dc96e3ce9) +- obi_clean was updated to [08d873cdd5f6](https://toolshed.g2.bx.psu.edu/view/iuc/obi_clean/08d873cdd5f6) +- obi_convert was updated to [e328ced6cf0a](https://toolshed.g2.bx.psu.edu/view/iuc/obi_convert/e328ced6cf0a) +- obi_grep was updated to [02bab5ff7c37](https://toolshed.g2.bx.psu.edu/view/iuc/obi_grep/02bab5ff7c37) +- obi_illumina_pairend was updated to [8cb6bd511879](https://toolshed.g2.bx.psu.edu/view/iuc/obi_illumina_pairend/8cb6bd511879) +- obi_ngsfilter was updated to [91a1ed0b486f](https://toolshed.g2.bx.psu.edu/view/iuc/obi_ngsfilter/91a1ed0b486f) +- obi_sort was updated to [b6d9ea2fb41b](https://toolshed.g2.bx.psu.edu/view/iuc/obi_sort/b6d9ea2fb41b) +- obi_stat was updated to [5f4544915893](https://toolshed.g2.bx.psu.edu/view/iuc/obi_stat/5f4544915893) +- obi_tab was updated to [4cf47c504672](https://toolshed.g2.bx.psu.edu/view/iuc/obi_tab/4cf47c504672) +- obi_uniq was updated to [d4bea99366f9](https://toolshed.g2.bx.psu.edu/view/iuc/obi_uniq/d4bea99366f9) + +## Ecoregionalization + +- ecoregion_brt_analysis was updated to [f0d6938d0451](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_brt_analysis/f0d6938d0451) +- ecoregion_brt_analysis was updated to [f8962f1c832a](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_brt_analysis/f8962f1c832a) +- ecoregion_clara_cluster was updated to [24a81631a8b5](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_clara_cluster/24a81631a8b5) +- ecoregion_cluster_estimate was updated to [0f6542d0986e](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_cluster_estimate/0f6542d0986e) +- ecoregion_cluster_estimate was updated to [1b9522671e90](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_cluster_estimate/1b9522671e90) +- ecoregion_eco_map was updated to [374555fc30bd](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_eco_map/374555fc30bd) +- ecoregion_taxa_seeker was updated to [788b118910a7](https://toolshed.g2.bx.psu.edu/view/ecology/ecoregion_taxa_seeker/788b118910a7) + +## QIIME 2 + +- qiime2__deblur__denoise_16S was updated to [2572fc0f88f2](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/2572fc0f88f2) +- qiime2__deblur__denoise_16S was updated to [b883cbea5623](https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2__deblur__denoise_16S/b883cbea5623) + +## Proteomics + +- maxquant was updated to [9c52362ae7bb](https://toolshed.g2.bx.psu.edu/view/galaxyp/maxquant/9c52362ae7bb) +- metaquantome_db was updated to [e63db1aa82ee](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_db/e63db1aa82ee) +- metaquantome_expand was updated to [767c1d761aaf](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_expand/767c1d761aaf) +- metaquantome_filter was updated to [35cc7ca0bdc7](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_filter/35cc7ca0bdc7) +- metaquantome_sample was updated to [06f6826d380c](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_sample/06f6826d380c) +- metaquantome_stat was updated to [b9d453dca8d3](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_stat/b9d453dca8d3) +- metaquantome_viz was updated to [8bd7734309f6](https://toolshed.g2.bx.psu.edu/view/galaxyp/metaquantome_viz/8bd7734309f6) +- openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) +- openms_percolatoradapter was updated to [0fc9ae55bcfc](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/0fc9ae55bcfc) +- openms_percolatoradapter was updated to [e7881a82b56d](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_percolatoradapter/e7881a82b56d) +- openms_xfdr was updated to [81402a5e4173](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/81402a5e4173) +- openms_xfdr was updated to [9a6e3bb0f358](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_xfdr/9a6e3bb0f358) + +## Metagenomic Analysis + +- metagene_annotator was updated to [17c7ab82bfbc](https://toolshed.g2.bx.psu.edu/view/galaxyp/metagene_annotator/17c7ab82bfbc) +- phyloseq_from_biom was updated to [c0101c72b8af](https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_biom/c0101c72b8af) +- srst2 was updated to [81cea47ec685](https://toolshed.g2.bx.psu.edu/view/iuc/srst2/81cea47ec685) +- virannot_blast2tsv was updated to [e889010415a1](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_blast2tsv/e889010415a1) +- virannot_otu was updated to [c9dac9b2e01c](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_otu/c9dac9b2e01c) +- virannot_rps2tsv was updated to [bbaa89f070f4](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_rps2tsv/bbaa89f070f4) + +## Annotation + +- repeatmodeler was updated to [4a172d211285](https://toolshed.g2.bx.psu.edu/view/csbl/repeatmodeler/4a172d211285) +- helixer was updated to [e3846dc36c4d](https://toolshed.g2.bx.psu.edu/view/genouest/helixer/e3846dc36c4d) +- abritamr was updated to [5aaffb8d8161](https://toolshed.g2.bx.psu.edu/view/iuc/abritamr/5aaffb8d8161) +- busco was updated to [ea8146ee148f](https://toolshed.g2.bx.psu.edu/view/iuc/busco/ea8146ee148f) +- mitos was updated to [e50a4f4542fc](https://toolshed.g2.bx.psu.edu/view/iuc/mitos/e50a4f4542fc) +- mitos2 was updated to [73b018c57e96](https://toolshed.g2.bx.psu.edu/view/iuc/mitos2/73b018c57e96) +- omark was updated to [6f570ba54b41](https://toolshed.g2.bx.psu.edu/view/iuc/omark/6f570ba54b41) +- red was updated to [db57bc3b57af](https://toolshed.g2.bx.psu.edu/view/iuc/red/db57bc3b57af) +- tsebra was updated to [681fd806acc4](https://toolshed.g2.bx.psu.edu/view/iuc/tsebra/681fd806acc4) + +## None + +- data_manager_diamond_database_builder was updated to [4a08b7b76b78](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78) +- data_manager_mapseq was updated to [4cd97cc67061](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_mapseq/4cd97cc67061) +- data_manager_omamer was updated to [e1502e4f8725](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_omamer/e1502e4f8725) + +## Evolution + +- revoluzer_crex was updated to [e0b7c98f29bb](https://toolshed.g2.bx.psu.edu/view/iuc/revoluzer_crex/e0b7c98f29bb) +- revoluzer_distmat was updated to [af7528402a97](https://toolshed.g2.bx.psu.edu/view/iuc/revoluzer_distmat/af7528402a97) + +## FASTA/FASTQ + +- cutadapt was updated to [944ae523bacb](https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/944ae523bacb) + +## Mapping + +- minimap2 was updated to [92678fcb1a5f](https://toolshed.g2.bx.psu.edu/view/iuc/minimap2/92678fcb1a5f) + +## Multiple Alignments + +- mummer_delta_filter was updated to [e8fdceffea4c](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_delta_filter/e8fdceffea4c) +- mummer_dnadiff was updated to [5561a1193611](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_dnadiff/5561a1193611) +- mummer_mummer was updated to [57f042937ba7](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_mummer/57f042937ba7) +- mummer_mummerplot was updated to [fb43e8887350](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_mummerplot/fb43e8887350) +- mummer_nucmer was updated to [7cd7a55a678d](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_nucmer/7cd7a55a678d) +- mummer_show_coords was updated to [cf3c9489c088](https://toolshed.g2.bx.psu.edu/view/iuc/mummer_show_coords/cf3c9489c088) + +## Phylogenetics + +- hyphy_prime was updated to [4072360120e4](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4) +- usher was updated to [335665e15630](https://toolshed.g2.bx.psu.edu/view/iuc/usher/335665e15630) +- usher was updated to [746b434c8fbb](https://toolshed.g2.bx.psu.edu/view/iuc/usher/746b434c8fbb) +- usher_matutils was updated to [79e2ee4e6ebb](https://toolshed.g2.bx.psu.edu/view/iuc/usher_matutils/79e2ee4e6ebb) +- usher_matutils was updated to [e0a0a473fc1e](https://toolshed.g2.bx.psu.edu/view/iuc/usher_matutils/e0a0a473fc1e) + +## RNA Analysis + +- salmon was updated to [f4d5237a84f6](https://toolshed.g2.bx.psu.edu/view/bgruening/salmon/f4d5237a84f6) +- salmonquantmerge was updated to [a896b8b7d264](https://toolshed.g2.bx.psu.edu/view/bgruening/salmonquantmerge/a896b8b7d264) + +## Single-cell + +- alevin was updated to [c9944a2600f1](https://toolshed.g2.bx.psu.edu/view/bgruening/alevin/c9944a2600f1) + +## hca_sc_scanpy_tools + +- seurat_plot was updated to [95d79f1134f0](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_plot/95d79f1134f0) +- seurat_run_umap was updated to [b9424c715a0d](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_run_umap/b9424c715a0d) +