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| --- | ||
| site: freiburg | ||
| tags: [tools] | ||
| title: UseGalaxy.eu Tool Updates for 2024-09-02 | ||
| supporters: | ||
| - denbi | ||
| - elixir | ||
| --- | ||
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| On 2024-09-02, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #472](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#472/) | ||
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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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| ## ChemicalToolBox | ||
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| - gmx_get_builtin_file was updated to [42dfec375136](https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_get_builtin_file/42dfec375136) | ||
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| ## Get Data | ||
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| - sra_tools was updated to [8848455c0270](https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/8848455c0270) | ||
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| ## Motif Tools | ||
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| - meme_fimo was updated to [01f5d04846c4](https://toolshed.g2.bx.psu.edu/view/iuc/meme_fimo/01f5d04846c4) | ||
| - meme_meme was updated to [7ce0fe11b411](https://toolshed.g2.bx.psu.edu/view/iuc/meme_meme/7ce0fe11b411) | ||
| - meme_meme was updated to [9dd5373f6a5a](https://toolshed.g2.bx.psu.edu/view/iuc/meme_meme/9dd5373f6a5a) | ||
| - meme_psp_gen was updated to [47e7ae719765](https://toolshed.g2.bx.psu.edu/view/iuc/meme_psp_gen/47e7ae719765) | ||
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| ## Proteomics | ||
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| - openms_idmassaccuracy was updated to [31bc4129f589](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_idmassaccuracy/31bc4129f589) | ||
| - openms_openpepxl was updated to [a2a842b00f9c](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxl/a2a842b00f9c) | ||
| - openms_openpepxllf was updated to [e574d3f268f6](https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_openpepxllf/e574d3f268f6) | ||
| - 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) | ||
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| ## Assembly | ||
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| - erga_ear was updated to [a34826ae0a73](https://toolshed.g2.bx.psu.edu/view/bgruening/erga_ear/a34826ae0a73) | ||
| - flye was updated to [3e4f8642c77e](https://toolshed.g2.bx.psu.edu/view/bgruening/flye/3e4f8642c77e) | ||
| - rnaquast was updated to [3125faf00ffd](https://toolshed.g2.bx.psu.edu/view/iuc/rnaquast/3125faf00ffd) | ||
| - rnaquast was updated to [f73ab5187eed](https://toolshed.g2.bx.psu.edu/view/iuc/rnaquast/f73ab5187eed) | ||
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| ## Graph/Display Data | ||
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| - jbrowse2 was updated to [b55199c56abd](https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/b55199c56abd) | ||
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| ## Machine Learning | ||
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| - keras_model_builder was updated to [8611b3f52a38](https://toolshed.g2.bx.psu.edu/view/bgruening/keras_model_builder/8611b3f52a38) | ||
| - keras_model_builder was updated to [9b6faa256f15](https://toolshed.g2.bx.psu.edu/view/bgruening/keras_model_builder/9b6faa256f15) | ||
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| ## Imaging | ||
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| - cp_convert_objects_to_image was updated to [d9fa2e6fae97](https://toolshed.g2.bx.psu.edu/view/bgruening/cp_convert_objects_to_image/d9fa2e6fae97) | ||
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| ## Annotation | ||
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| - busco was updated to [2babe6d5c561](https://toolshed.g2.bx.psu.edu/view/iuc/busco/2babe6d5c561) | ||
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| ## FASTA/FASTQ | ||
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| - adapter_removal was updated to [40874f772ea1](https://toolshed.g2.bx.psu.edu/view/iuc/adapter_removal/40874f772ea1) | ||
| - bbtools_bbduk was updated to [7beb76ffbc0f](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbduk/7beb76ffbc0f) | ||
| - bbtools_bbmerge was updated to [cab19c0452c4](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmerge/cab19c0452c4) | ||
| - bbtools_tadpole was updated to [0ddf147d1897](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_tadpole/0ddf147d1897) | ||
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| ## Mapping | ||
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| - bbtools_bbmap was updated to [456d8ebb6a28](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_bbmap/456d8ebb6a28) | ||
| - rna_starsolo was updated to [45795f582ae9](https://toolshed.g2.bx.psu.edu/view/iuc/rna_starsolo/45795f582ae9) | ||
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| ## Metagenomic Analysis | ||
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| - ampvis2_alpha_diversity was updated to [289d6299bd2e](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_alpha_diversity/289d6299bd2e) | ||
| - ampvis2_boxplot was updated to [b3c5560ffac6](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_boxplot/b3c5560ffac6) | ||
| - ampvis2_core was updated to [2bbf288d6334](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_core/2bbf288d6334) | ||
| - ampvis2_export_fasta was updated to [0cce683798d3](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_export_fasta/0cce683798d3) | ||
| - ampvis2_frequency was updated to [f309f1ef68f3](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_frequency/f309f1ef68f3) | ||
| - ampvis2_heatmap was updated to [9bdb74297b3d](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_heatmap/9bdb74297b3d) | ||
| - ampvis2_load was updated to [576dd33588bf](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_load/576dd33588bf) | ||
| - ampvis2_merge_ampvis2 was updated to [2f9731cc4c87](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_merge_ampvis2/2f9731cc4c87) | ||
| - ampvis2_mergereplicates was updated to [1f6f3bc6edd1](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_mergereplicates/1f6f3bc6edd1) | ||
| - ampvis2_octave was updated to [a0a792d4efae](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_octave/a0a792d4efae) | ||
| - ampvis2_ordinate was updated to [7c675dae82eb](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_ordinate/7c675dae82eb) | ||
| - ampvis2_otu_network was updated to [454bfdfa6de5](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_otu_network/454bfdfa6de5) | ||
| - ampvis2_rankabundance was updated to [18de61c5527c](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rankabundance/18de61c5527c) | ||
| - ampvis2_rarecurve was updated to [cfa509a60770](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_rarecurve/cfa509a60770) | ||
| - ampvis2_setmetadata was updated to [cfd7bafb820f](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_setmetadata/cfd7bafb820f) | ||
| - ampvis2_subset_samples was updated to [f9fa155c191f](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_samples/f9fa155c191f) | ||
| - ampvis2_subset_taxa was updated to [cf579d6919e8](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_subset_taxa/cf579d6919e8) | ||
| - ampvis2_timeseries was updated to [f41dad652845](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_timeseries/f41dad652845) | ||
| - ampvis2_venn was updated to [bbb4a531d80b](https://toolshed.g2.bx.psu.edu/view/iuc/ampvis2_venn/bbb4a531d80b) | ||
| - biobox_add_taxid was updated to [1e10251b9615](https://toolshed.g2.bx.psu.edu/view/iuc/biobox_add_taxid/1e10251b9615) | ||
| - cami_amber was updated to [9ed513717fc4](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber/9ed513717fc4) | ||
| - cami_amber was updated to [f801b844f239](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber/f801b844f239) | ||
| - cami_amber_add was updated to [2e6ddf48a213](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_add/2e6ddf48a213) | ||
| - cami_amber_add was updated to [433fb72344cb](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_add/433fb72344cb) | ||
| - cami_amber_convert was updated to [848594e0be6a](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/848594e0be6a) | ||
| - cami_amber_convert was updated to [8f0e53330d8e](https://toolshed.g2.bx.psu.edu/view/iuc/cami_amber_convert/8f0e53330d8e) | ||
| - gtdb_to_taxdump was updated to [102852801457](https://toolshed.g2.bx.psu.edu/view/iuc/gtdb_to_taxdump/102852801457) | ||
| - name2taxid was updated to [99ef57d30bfc](https://toolshed.g2.bx.psu.edu/view/iuc/name2taxid/99ef57d30bfc) | ||
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| ## Mothur | ||
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| - mothur_filter_shared was updated to [79f24f4ee6b6](https://toolshed.g2.bx.psu.edu/view/iuc/mothur_filter_shared/79f24f4ee6b6) | ||
| - mothur_filter_shared was updated to [e44c38a17c7a](https://toolshed.g2.bx.psu.edu/view/iuc/mothur_filter_shared/e44c38a17c7a) | ||
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| ## Nanopore | ||
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| - ont_fast5_api_fast5_subset was updated to [3bdd8fa109b1](https://toolshed.g2.bx.psu.edu/view/iuc/ont_fast5_api_fast5_subset/3bdd8fa109b1) | ||
| - ont_fast5_api_multi_to_single_fast5 was updated to [1a37f742e7d7](https://toolshed.g2.bx.psu.edu/view/iuc/ont_fast5_api_multi_to_single_fast5/1a37f742e7d7) | ||
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| ## Phylogenetics | ||
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| - hyphy_prime was updated to [4072360120e4](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4) | ||
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| ## RAD-seq | ||
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| - stacks_refmap was updated to [7c42e6768c41](https://toolshed.g2.bx.psu.edu/view/iuc/stacks_refmap/7c42e6768c41) | ||
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| ## SAM/BAM | ||
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| - samtools_view was updated to [2dce91e11ca7](https://toolshed.g2.bx.psu.edu/view/iuc/samtools_view/2dce91e11ca7) | ||
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| ## Single-cell | ||
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| - infercnv was updated to [ddbace8f3277](https://toolshed.g2.bx.psu.edu/view/iuc/infercnv/ddbace8f3277) | ||
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| ## Variant Calling | ||
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| - bbtools_callvariants was updated to [7e041c120b96](https://toolshed.g2.bx.psu.edu/view/iuc/bbtools_callvariants/7e041c120b96) | ||
| - bcftools_query was updated to [a850902cac64](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/a850902cac64) | ||
| - bcftools_query was updated to [c9c5718edc19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/c9c5718edc19) | ||
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| ## Virology | ||
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| - virheat was updated to [b5411b5e8259](https://toolshed.g2.bx.psu.edu/view/iuc/virheat/b5411b5e8259) | ||
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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) | ||
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| ## hca_sc_scanpy_tools | ||
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| - scanpy_filter_cells was updated to [26a98de26847](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_filter_cells/26a98de26847) | ||
| - scanpy_filter_cells was updated to [3dcc1629e420](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/scanpy_filter_cells/3dcc1629e420) | ||
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