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| --- | ||
| site: freiburg | ||
| tags: [tools] | ||
| title: UseGalaxy.eu Tool Updates for 2023-11-12 | ||
| supporters: | ||
| - denbi | ||
| - elixir | ||
| --- | ||
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| On 2023-11-12, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in [Jenkins Build #416](https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#416/) | ||
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| ## Join, Subtract and Group | ||
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| - datamash_transpose was updated to [a513e3fbb4c5](https://toolshed.g2.bx.psu.edu/view/iuc/datamash_transpose/a513e3fbb4c5) | ||
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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) | ||
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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) | ||
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| ## Imaging | ||
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| - cp_cellprofiler4 was updated to [f0656d0f2a4d](https://toolshed.g2.bx.psu.edu/view/bgruening/cp_cellprofiler4/f0656d0f2a4d) | ||
| - 2d_auto_threshold was updated to [3df9f0a4bf34](https://toolshed.g2.bx.psu.edu/view/imgteam/2d_auto_threshold/3df9f0a4bf34) | ||
| - 2d_feature_extraction was updated to [0a53256b48c6](https://toolshed.g2.bx.psu.edu/view/imgteam/2d_feature_extraction/0a53256b48c6) | ||
| - 2d_simple_filter was updated to [f70b215d155c](https://toolshed.g2.bx.psu.edu/view/imgteam/2d_simple_filter/f70b215d155c) | ||
| - bfconvert was updated to [85edbb7a436b](https://toolshed.g2.bx.psu.edu/view/imgteam/bfconvert/85edbb7a436b) | ||
| - image_info was updated to [236ec78b2e53](https://toolshed.g2.bx.psu.edu/view/imgteam/image_info/236ec78b2e53) | ||
| - mahotas_features was updated to [0c76d029dbe3](https://toolshed.g2.bx.psu.edu/view/imgteam/mahotas_features/0c76d029dbe3) | ||
| - overlay_images was updated to [22ff7c705a83](https://toolshed.g2.bx.psu.edu/view/imgteam/overlay_images/22ff7c705a83) | ||
| - scale_image was updated to [d09507d3fb0e](https://toolshed.g2.bx.psu.edu/view/imgteam/scale_image/d09507d3fb0e) | ||
| - visceral_evaluatesegmentation was updated to [4d042d197ac3](https://toolshed.g2.bx.psu.edu/view/imgteam/visceral_evaluatesegmentation/4d042d197ac3) | ||
| - idr_download_by_ids was updated to [4b794652dcdc](https://toolshed.g2.bx.psu.edu/view/iuc/idr_download_by_ids/4b794652dcdc) | ||
| - spyboat was updated to [117a042eb1b8](https://toolshed.g2.bx.psu.edu/view/iuc/spyboat/117a042eb1b8) | ||
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| ## Annotation | ||
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| - repeatmodeler was updated to [fbe22cb3c869](https://toolshed.g2.bx.psu.edu/view/csbl/repeatmodeler/fbe22cb3c869) | ||
| - hmmer_alimask was updated to [3734a6ad6363](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_alimask/3734a6ad6363) | ||
| - hmmer_hmmalign was updated to [9319e9ed248b](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmalign/9319e9ed248b) | ||
| - hmmer_hmmbuild was updated to [923db0592cd0](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmbuild/923db0592cd0) | ||
| - hmmer_hmmconvert was updated to [d20066f6566e](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmconvert/d20066f6566e) | ||
| - hmmer_hmmemit was updated to [e9d622609fb5](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmemit/e9d622609fb5) | ||
| - hmmer_hmmfetch was updated to [1fca13688921](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmfetch/1fca13688921) | ||
| - hmmer_hmmscan was updated to [347a1f935f4c](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmscan/347a1f935f4c) | ||
| - hmmer_hmmsearch was updated to [3bb58751f4ee](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_hmmsearch/3bb58751f4ee) | ||
| - hmmer_jackhmmer was updated to [5cbef50c0c63](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_jackhmmer/5cbef50c0c63) | ||
| - hmmer_nhmmer was updated to [2ec5e1ad1da7](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_nhmmer/2ec5e1ad1da7) | ||
| - hmmer_nhmmscan was updated to [e7d281a290a6](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_nhmmscan/e7d281a290a6) | ||
| - hmmer_phmmer was updated to [92ff5dcded40](https://toolshed.g2.bx.psu.edu/view/iuc/hmmer_phmmer/92ff5dcded40) | ||
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| ## Assembly | ||
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| - hifiasm was updated to [0ee0c3089254](https://toolshed.g2.bx.psu.edu/view/bgruening/hifiasm/0ee0c3089254) | ||
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| ## Collection Operations | ||
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| - pick_value was updated to [bf793b71559a](https://toolshed.g2.bx.psu.edu/view/iuc/pick_value/bf793b71559a) | ||
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| ## Metagenomic Analysis | ||
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| - lotus2 was updated to [ceb2cb800298](https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/ceb2cb800298) | ||
| - drep_compare was updated to [ffeabd4e2c1b](https://toolshed.g2.bx.psu.edu/view/iuc/drep_compare/ffeabd4e2c1b) | ||
| - drep_dereplicate was updated to [a248ec535518](https://toolshed.g2.bx.psu.edu/view/iuc/drep_dereplicate/a248ec535518) | ||
| - metabat2 was updated to [eb50e7eca3dc](https://toolshed.g2.bx.psu.edu/view/iuc/metabat2/eb50e7eca3dc) | ||
| - metabat2_jgi_summarize_bam_contig_depths was updated to [ec045ca00b50](https://toolshed.g2.bx.psu.edu/view/iuc/metabat2_jgi_summarize_bam_contig_depths/ec045ca00b50) | ||
| - semibin was updated to [99ff9221182c](https://toolshed.g2.bx.psu.edu/view/iuc/semibin/99ff9221182c) | ||
| - semibin_bin was updated to [dbf5571a8140](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_bin/dbf5571a8140) | ||
| - semibin_concatenate_fasta was updated to [298542e0e136](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_concatenate_fasta/298542e0e136) | ||
| - semibin_generate_cannot_links was updated to [a6f004bc73bf](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_generate_cannot_links/a6f004bc73bf) | ||
| - semibin_generate_sequence_features was updated to [ff4e487f4f7e](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_generate_sequence_features/ff4e487f4f7e) | ||
| - semibin_train was updated to [8b77643cf479](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_train/8b77643cf479) | ||
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| ## SAM/BAM | ||
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| - mosdepth was updated to [efd53f6ceb16](https://toolshed.g2.bx.psu.edu/view/iuc/mosdepth/efd53f6ceb16) | ||
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| ## Single-cell | ||
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| - scanpy_cluster_reduce_dimension was updated to [edec35114f72](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_cluster_reduce_dimension/edec35114f72) | ||
| - scanpy_filter was updated to [2d02d9702d3a](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_filter/2d02d9702d3a) | ||
| - scanpy_inspect was updated to [6bd82ed14acd](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/6bd82ed14acd) | ||
| - scanpy_normalize was updated to [c9cb76cf8d6c](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_normalize/c9cb76cf8d6c) | ||
| - scanpy_plot was updated to [95777145cb92](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_plot/95777145cb92) | ||
| - scanpy_remove_confounders was updated to [73ab2ac53d06](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/73ab2ac53d06) | ||
| - sceasy_convert was updated to [d70139524747](https://toolshed.g2.bx.psu.edu/view/iuc/sceasy_convert/d70139524747) | ||
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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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| ## Metabolomics | ||
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| - mzmine_batch was updated to [90d60c9da21e](https://toolshed.g2.bx.psu.edu/view/iuc/mzmine_batch/90d60c9da21e) | ||
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| ## hca_sc_label_analysis_tools | ||
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| - decoupler_pseudobulk was updated to [4fa5f370599f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/decoupler_pseudobulk/4fa5f370599f) | ||
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