From 0ad141b43fc11dc1b79567f6a386183dfecf782b Mon Sep 17 00:00:00 2001 From: "UseGalaxy.EU Jenkins Bot" Date: Mon, 2 Sep 2024 13:34:22 +0200 Subject: [PATCH] Autoupdate tool blog post --- _posts/2024-09-02-tool-update.md | 154 +++++++++++++++++++++++++++++++ 1 file changed, 154 insertions(+) create mode 100644 _posts/2024-09-02-tool-update.md diff --git a/_posts/2024-09-02-tool-update.md b/_posts/2024-09-02-tool-update.md new file mode 100644 index 00000000..d4826317 --- /dev/null +++ b/_posts/2024-09-02-tool-update.md @@ -0,0 +1,154 @@ +--- +site: freiburg +tags: [tools] +title: UseGalaxy.eu Tool Updates for 2024-09-02 +supporters: +- denbi +- elixir +--- + +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/) + + +## 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) + +## ChemicalToolBox + +- gmx_get_builtin_file was updated to [42dfec375136](https://toolshed.g2.bx.psu.edu/view/chemteam/gmx_get_builtin_file/42dfec375136) + +## Get Data + +- sra_tools was updated to [8848455c0270](https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/8848455c0270) + +## Motif Tools + +- 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) + +## Proteomics + +- 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) + +## Assembly + +- 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) + +## Graph/Display Data + +- jbrowse2 was updated to [b55199c56abd](https://toolshed.g2.bx.psu.edu/view/fubar/jbrowse2/b55199c56abd) + +## Machine Learning + +- 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) + +## Imaging + +- cp_convert_objects_to_image was updated to [d9fa2e6fae97](https://toolshed.g2.bx.psu.edu/view/bgruening/cp_convert_objects_to_image/d9fa2e6fae97) + +## Annotation + +- busco was updated to [2babe6d5c561](https://toolshed.g2.bx.psu.edu/view/iuc/busco/2babe6d5c561) + +## FASTA/FASTQ + +- 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) + +## Mapping + +- 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) + +## Metagenomic Analysis + +- 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) + +## Mothur + +- 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) + +## Nanopore + +- 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) + +## Phylogenetics + +- hyphy_prime was updated to [4072360120e4](https://toolshed.g2.bx.psu.edu/view/iuc/hyphy_prime/4072360120e4) + +## RAD-seq + +- stacks_refmap was updated to [7c42e6768c41](https://toolshed.g2.bx.psu.edu/view/iuc/stacks_refmap/7c42e6768c41) + +## SAM/BAM + +- samtools_view was updated to [2dce91e11ca7](https://toolshed.g2.bx.psu.edu/view/iuc/samtools_view/2dce91e11ca7) + +## Single-cell + +- infercnv was updated to [ddbace8f3277](https://toolshed.g2.bx.psu.edu/view/iuc/infercnv/ddbace8f3277) + +## Variant Calling + +- 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) + +## Virology + +- virheat was updated to [b5411b5e8259](https://toolshed.g2.bx.psu.edu/view/iuc/virheat/b5411b5e8259) + +## None + +- data_manager_diamond_database_builder was updated to [4a08b7b76b78](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_diamond_database_builder/4a08b7b76b78) + +## hca_sc_scanpy_tools + +- 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) +