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| --- | ||
| site: freiburg | ||
| tags: [tools] | ||
| title: UseGalaxy.eu Tool Updates for 2024-08-25 | ||
| supporters: | ||
| - denbi | ||
| - elixir | ||
| --- | ||
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| On 2024-08-25, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #471](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#471/) | ||
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| ## Text Manipulation | ||
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| - column_maker was updated to [aff5135563c6](https://toolshed.g2.bx.psu.edu/view/devteam/column_maker/aff5135563c6) | ||
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| ## QIIME 2 | ||
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| - 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) | ||
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| ## Variant Calling | ||
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| - bcftools_annotate was updated to [2c372041ed8c](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/2c372041ed8c) | ||
| - bcftools_call was updated to [07396b423218](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/07396b423218) | ||
| - bcftools_cnv was updated to [ccb83bf54de0](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_cnv/ccb83bf54de0) | ||
| - bcftools_concat was updated to [05f317e50e61](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/05f317e50e61) | ||
| - bcftools_consensus was updated to [8aa352093d73](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_consensus/8aa352093d73) | ||
| - bcftools_convert_from_vcf was updated to [012656fd329f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/012656fd329f) | ||
| - bcftools_convert_to_vcf was updated to [cfd81f17580b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_to_vcf/cfd81f17580b) | ||
| - bcftools_csq was updated to [d237eaef451f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_csq/d237eaef451f) | ||
| - bcftools_filter was updated to [46fcafba49ec](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/46fcafba49ec) | ||
| - bcftools_gtcheck was updated to [7b4454382d39](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/7b4454382d39) | ||
| - bcftools_isec was updated to [39bca000353d](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/39bca000353d) | ||
| - bcftools_merge was updated to [5b006286a458](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/5b006286a458) | ||
| - bcftools_norm was updated to [271965b55437](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_norm/271965b55437) | ||
| - bcftools_plugin_color_chrs was updated to [7d9166ecd10f](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_color_chrs/7d9166ecd10f) | ||
| - bcftools_plugin_frameshifts was updated to [b03c0b3e67a6](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_frameshifts/b03c0b3e67a6) | ||
| - bcftools_plugin_setgt was updated to [a730269af659](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_setgt/a730269af659) | ||
| - bcftools_plugin_split_vep was updated to [7b71281eb0ca](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_split_vep/7b71281eb0ca) | ||
| - bcftools_query was updated to [31a1b89eab9b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/31a1b89eab9b) | ||
| - bcftools_reheader was updated to [2331ddcbd5aa](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/2331ddcbd5aa) | ||
| - bcftools_roh was updated to [fa65af07ce7d](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/fa65af07ce7d) | ||
| - bcftools_stats was updated to [591cc8518033](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_stats/591cc8518033) | ||
| - bcftools_view was updated to [1a2ef636f48e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/1a2ef636f48e) | ||
| - beacon2_analyses was updated to [2e057dfe494c](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_analyses/2e057dfe494c) | ||
| - beacon2_biosamples was updated to [5fedf42a718b](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_biosamples/5fedf42a718b) | ||
| - beacon2_bracket was updated to [3347fc9c43bf](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_bracket/3347fc9c43bf) | ||
| - beacon2_cnv was updated to [398000f8de7d](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_cnv/398000f8de7d) | ||
| - beacon2_cohorts was updated to [d524bd42b89e](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_cohorts/d524bd42b89e) | ||
| - beacon2_datasets was updated to [1f9f549aa9ca](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_datasets/1f9f549aa9ca) | ||
| - beacon2_gene was updated to [9135f3e914b7](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_gene/9135f3e914b7) | ||
| - beacon2_import was updated to [d2646a23f6b2](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_import/d2646a23f6b2) | ||
| - beacon2_individuals was updated to [72d8cb0fa73f](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_individuals/72d8cb0fa73f) | ||
| - beacon2_range was updated to [5bb5861b37b6](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_range/5bb5861b37b6) | ||
| - beacon2_runs was updated to [016fc58daa80](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_runs/016fc58daa80) | ||
| - beacon2_sequence was updated to [4818fff6105d](https://toolshed.g2.bx.psu.edu/view/iuc/beacon2_sequence/4818fff6105d) | ||
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| ## Proteomics | ||
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| - openms_openpepxl was updated to [40cc19c0dbd6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/40cc19c0dbd6) | ||
| - openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) | ||
| - openms_openpepxl was updated to [fc36cfd19834](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/fc36cfd19834) | ||
| - 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) | ||
| - prot_scriber was updated to [f05dfa43240f](https://toolshed.g2.bx.psu.edu/view/iuc/prot_scriber/f05dfa43240f) | ||
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| ## Convert Formats | ||
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| - graphicsmagick_image_compare was updated to [cfe1d6e23237](https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_compare/cfe1d6e23237) | ||
| - graphicsmagick_image_convert was updated to [3ae9331790a6](https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_convert/3ae9331790a6) | ||
| - graphicsmagick_image_montage was updated to [3e81299dfce3](https://toolshed.g2.bx.psu.edu/view/bgruening/graphicsmagick_image_montage/3e81299dfce3) | ||
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| ## Imaging | ||
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| - cellpose was updated to [9186100e75b5](https://toolshed.g2.bx.psu.edu/view/bgruening/cellpose/9186100e75b5) | ||
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| ## Machine Learning | ||
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| - chatgpt_openai_api was updated to [dab494dce303](https://toolshed.g2.bx.psu.edu/view/bgruening/chatgpt_openai_api/dab494dce303) | ||
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| ## Multiple Alignments | ||
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| - mafft was updated to [8e649f27aa0d](https://toolshed.g2.bx.psu.edu/view/rnateam/mafft/8e649f27aa0d) | ||
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| ## None | ||
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| - 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_omamer was updated to [e1502e4f8725](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_omamer/e1502e4f8725) | ||
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| ## Evolution | ||
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| - iqtree was updated to [0878b7fd5260](https://toolshed.g2.bx.psu.edu/view/iuc/iqtree/0878b7fd5260) | ||
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| ## FASTA/FASTQ | ||
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| - ncbi_fcs_gx was updated to [c228e49365c4](https://toolshed.g2.bx.psu.edu/view/iuc/ncbi_fcs_gx/c228e49365c4) | ||
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| ## Metagenomic Analysis | ||
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| - dram_annotate was updated to [df8dac817fc8](https://toolshed.g2.bx.psu.edu/view/iuc/dram_annotate/df8dac817fc8) | ||
| - dram_distill was updated to [e12898633ceb](https://toolshed.g2.bx.psu.edu/view/iuc/dram_distill/e12898633ceb) | ||
| - dram_merge_annotations was updated to [ca2c752a22e4](https://toolshed.g2.bx.psu.edu/view/iuc/dram_merge_annotations/ca2c752a22e4) | ||
| - dram_neighborhoods was updated to [877bdba8fc5d](https://toolshed.g2.bx.psu.edu/view/iuc/dram_neighborhoods/877bdba8fc5d) | ||
| - dram_strainer was updated to [f081f73cc0be](https://toolshed.g2.bx.psu.edu/view/iuc/dram_strainer/f081f73cc0be) | ||
| - humann2_barplot was updated to [56cb2b0269d1](https://toolshed.g2.bx.psu.edu/view/iuc/humann2_barplot/56cb2b0269d1) | ||
| - virannot_blast2tsv was updated to [77c3ef9b0ed7](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_blast2tsv/77c3ef9b0ed7) | ||
| - virannot_otu was updated to [735a21808348](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_otu/735a21808348) | ||
| - virannot_rps2tsv was updated to [fd7104249a3c](https://toolshed.g2.bx.psu.edu/view/iuc/virannot_rps2tsv/fd7104249a3c) | ||
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| ## Phylogenetics | ||
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| - hyphy_annotate was updated to [ec59f7a36a24](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_annotate/ec59f7a36a24) | ||
| - hyphy_prime was updated to [4072360120e4](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4) | ||
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| ## RNA Analysis | ||
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| - brew3r_r was updated to [3198f52bffaa](https://toolshed.g2.bx.psu.edu/view/iuc/brew3r_r/3198f52bffaa) | ||
| - cemitool was updated to [9d93999d9028](https://toolshed.g2.bx.psu.edu/view/iuc/cemitool/9d93999d9028) | ||
| - locarna_multiple was updated to [6e20ad2c8752](https://toolshed.g2.bx.psu.edu/view/rnateam/locarna_multiple/6e20ad2c8752) | ||
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| ## Single-cell | ||
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| - scanpy_cluster_reduce_dimension was updated to [f9353ee6a0d4](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_cluster_reduce_dimension/f9353ee6a0d4) | ||
| - scanpy_filter was updated to [72a6bebab2a5](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_filter/72a6bebab2a5) | ||
| - scanpy_inspect was updated to [c0a80a16560f](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/c0a80a16560f) | ||
| - scanpy_normalize was updated to [9f354c7c8c92](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_normalize/9f354c7c8c92) | ||
| - scanpy_plot was updated to [1072ce66b426](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_plot/1072ce66b426) | ||
| - scanpy_remove_confounders was updated to [a39040ae0a38](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/a39040ae0a38) | ||
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| ## Statistics | ||
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| - clustering_from_distmat was updated to [c0b01c55a0e0](https://toolshed.g2.bx.psu.edu/view/iuc/clustering_from_distmat/c0b01c55a0e0) | ||
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| ## Metabolomics | ||
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| - tracegroomer was updated to [ea6ea4029c47](https://toolshed.g2.bx.psu.edu/view/iuc/tracegroomer/ea6ea4029c47) | ||
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