On 2022-01-14, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #304

Graph/Display Data

• bandage was updated to b9e31c5c01c7
• circos was updated to 290a11559985
• ggplot2_heatmap was updated to d3a9e32672ec
• ggplot2_histogram was updated to 355a82227003
• ggplot2_point was updated to 1acf88921176
• ggplot2_violin was updated to e44775efb2dc

RAD-seq

• stacks2_denovomap was updated to ad5ab22ffe24
• stacks2_gstacks was updated to eb784fa07f80
• stacks2_kmerfilter was updated to 1544278c272e
• stacks2_populations was updated to 887cf585cafc
• stacks2_procrad was updated to e897c74a48bb
• stacks2_refmap was updated to 4f65e343ecdf
• stacks2_shortreads was updated to c5d7050e4ad7
• stacks2_sstacks was updated to cd034465d4a4
• stacks2_ustacks was updated to cfb504394ae1

ChemicalToolBox

• autodock_vina was updated to 90ea16534012
• ctb_rdkit_descriptors was updated to 0993ac4f4a23
• ambertools_antechamber was updated to 4fff93efc0f9
• ambertools_antechamber was updated to c280abd461a6
• gmx_editconf was updated to 79cfd9ead848
• gmx_em was updated to 59c662ca4211
• gmx_em was updated to 715cd0e87781
• gmx_energy was updated to 58c3e6711e94
• gmx_energy was updated to fdf2cc80adb5
• gmx_makendx was updated to 358747bce4fd
• gmx_merge_topology_files was updated to 3cf3b3b305ea
• gmx_restraints was updated to 14a7bf3e03df
• gmx_restraints was updated to 9dde06738154
• gmx_rg was updated to f360f62ac4c4
• gmx_setup was updated to 1d4dd4f908d4
• gmx_setup was updated to ed736e6eee39
• gmx_sim was updated to d1f803b5943c
• gmx_solvate was updated to 7568ae18908a
• gmx_trj was updated to 16fad30d566a
• gmx_trj was updated to 240834a8b602
• mmpbsa_mmgbsa was updated to 12caa50c0d5f
• traj_selections_and_merge was updated to a26c4750c7c7

RNA Analysis

• chira_collapse was updated to 05996586c8b3
• chira_extract was updated to 73d2b7a8d94b
• chira_map was updated to 7925dd016f53
• chira_merge was updated to 9930af9d17f8
• chira_quantify was updated to 38d2b1f38992
• dexseq was updated to 2872c633f07e
• edger was updated to df0c8d0a5992
• edger was updated to f2843df56434
• genomic_super_signature was updated to d0cbe6cc1f04
• limma_voom was updated to 32511f586472
• limma_voom was updated to e827f9aae031
• seurat was updated to bb9732cfcdbe
• trinity was updated to d2bc35f3d1c5
• trinity_abundance_estimates_to_matrix was updated to 2e21a7c28b38
• trinity_abundance_estimates_to_matrix was updated to bcc5f03f1900
• trinity_align_and_estimate_abundance was updated to 00719b8004c9
• trinity_align_and_estimate_abundance was updated to c2b82a94493e
• trinity_contig_exn50_statistic was updated to 34840e9c79b0
• trinity_contig_exn50_statistic was updated to be3f26533209
• trinity_filter_low_expr_transcripts was updated to 1007cdb58d91
• trinity_filter_low_expr_transcripts was updated to 1fdb25a8384d
• trinity_run_de_analysis was updated to 3bff7c3cf63c
• trinity_run_de_analysis was updated to eafea3083352
• trinity_super_transcripts was updated to 18a069ea4b96
• trinity_super_transcripts was updated to bdede464821e
• trinotate was updated to 2b093007fab9

Epigenetics

• bwameth was updated to 62f5fab76dfb

Proteomics

• maxquant_mqpar was updated to 2d67fb758956
• maxquant_mqpar was updated to 9cb7dcc07dae
• metaquantome_sample was updated to c1343e3389ca
• openms_openpepxl was updated to 40cc19c0dbd6
• openms_openpepxl was updated to a2a842b00f9c
• openms_openpepxl was updated to fc36cfd19834
• openms_percolatoradapter was updated to 0fc9ae55bcfc
• openms_percolatoradapter was updated to e7881a82b56d
• openms_xfdr was updated to 4fdeb75928ea
• openms_xfdr was updated to 81402a5e4173
• openms_xfdr was updated to 9a6e3bb0f358
• pepquery was updated to 962599ac5406
• peptideshaker was updated to a6ff76e057fd
• proteinortho was updated to 9b99159b2b23
• proteinortho_grab_proteins was updated to 6eec1c6410fe
• proteinortho_grab_proteins was updated to d5e4450964f8
• proteinortho_summary was updated to 1883d2bffd14

Assembly

• abyss was updated to 890b794c997d
• minia was updated to 734cd5f1c1b2
• novoplasty was updated to 15200570e926
• quast was updated to 7594365c546b
• raven was updated to f11b994b7eb2
• trycycler_cluster was updated to 189e837009c9
• trycycler_cluster was updated to 505a9833ab5d
• trycycler_consensus was updated to 43af166bc01e
• trycycler_consensus was updated to 9ded6109434a
• trycycler_partition was updated to b23249f81bc4
• trycycler_reconcile_msa was updated to 59bd28f6265d
• trycycler_subsample was updated to 05bd7504fdb2

hca_sc_scanpy_tools

• anndata_ops was updated to 890fb06a2893

Imaging

• points_association_nn was updated to fd4293bee0dc
• spot_detection_2d was updated to d78372040976
• idr_download_by_ids was updated to 4aed70472589

Metagenomic Analysis

• data_manager_build_bracken_database was updated to 3c7d2c84cb09
• data_manager_build_bracken_database was updated to fd5830f88314
• last was updated to 19c265784f35
• megan_blast2lca was updated to a80281b0172e
• megan_blast2rma was updated to d326b943f5e2
• megan_sam2rma was updated to 4f0a8e401e2e

Annotation

• repeatmodeler was updated to 41bfbaf3c959
• funannotate_annotate was updated to 14f588312c56
• funannotate_clean was updated to a230ea445788
• funannotate_compare was updated to 563a19373357
• funannotate_predict was updated to 2bba2ff070d9
• funannotate_sort was updated to b3cf4684e9c7
• gff_to_prot was updated to 07d7991bf205
• gff_to_prot was updated to 79261884facd
• homer_annotatepeaks was updated to 35dc2f57d755
• homer_findmotifsgenome was updated to a8f207b43f64
• homer_gtf_to_annotations was updated to 396cf2c12173
• homer_scanmotifgenomewide was updated to db456c398880
• orthofinder_onlygroups was updated to 3b974afde673
• progressivemauve was updated to ce795616bd9c
• transit_gumbel was updated to 8fc50fe60127
• transit_resampling was updated to 885459e1c83b
• transit_tn5gaps was updated to 3f5fc4b09496

Nanopore

• flair_collapse was updated to 1fdcbfcca71c

Single-cell

• raceid_clustering was updated to c4f39bf4a068
• raceid_clustering was updated to f911a64454fb
• raceid_filtnormconf was updated to c891d8b33ede
• raceid_filtnormconf was updated to d45f092caf24
• raceid_inspectclusters was updated to 2b0d3e2f402a
• raceid_inspectclusters was updated to be4646256624
• raceid_inspecttrajectory was updated to 3478133d0f6f
• raceid_inspecttrajectory was updated to df8e4e54d367
• raceid_trajectory was updated to c92d0f9338c5
• raceid_trajectory was updated to e93b008c637a

Variant Calling

• freebayes was updated to 04fa42777df9
• freebayes was updated to 57def2d7c093
• vcfcheck was updated to 2968c6916579
• vcfcheck was updated to aa8e8c96ca06
• artic_guppyplex was updated to 5ceeb5a5d70f
• artic_guppyplex was updated to 7a82006f7c05
• artic_minion was updated to 7a7d7f30ddfc
• artic_minion was updated to f212134e204c
• bbtools_callvariants was updated to b955346ef41e
• delly_call was updated to 6f383714149d
• delly_classify was updated to d31211a43b19
• delly_cnv was updated to 56781a718729
• delly_filter was updated to d2590fe6793f
• delly_lr was updated to d30785dbe6b7
• delly_merge was updated to 1efb2b927957
• plink was updated to 16d22eee0fe3
• plink was updated to 272aca44b3dd
• seqwish was updated to 36dc42da5687
• varscan_copynumber was updated to 0bc56f894766
• varscan_copynumber was updated to 9f8dbbbc0267
• varscan_mpileup was updated to 45288fb1f3f5
• varscan_somatic was updated to a57606054bd7
• varscan_somatic was updated to cf8ffc79db67
• vcfanno was updated to cdcaa40e5e45

Evolution

• codeml was updated to f9cb3a4339c2
• iqtree was updated to 563c3aa769f2
• iqtree was updated to 9b892d7f82cc

Convert Formats

• crossmap_bam was updated to e13f565068d6
• genebed_maf_to_fasta was updated to 020c78e91cc5
• genebed_maf_to_fasta was updated to e25ee6bac872

FASTA/FASTQ

• fastx_clipper was updated to b8658f852bc7
• fastx_clipper was updated to cb1e251cac37
• fasta_stats was updated to 16f1f3e2de42
• fasta_stats was updated to cd0874854f51
• cutadapt was updated to c053d4cad713

Motif Tools

• meme_chip was updated to 091a9d638d78
• meme_chip was updated to cc100e0f61f4

Multiple Alignments

• mummer_delta_filter was updated to fbca557a4847
• mummer_dnadiff was updated to c9685bc0407c
• mummer_nucmer was updated to e18267f90096

Mapping

• bbtools_bbmap was updated to e0ca2ec4f5d9
• bioext_bealign was updated to 09dbbf5d3201
• bioext_bealign was updated to a07a2d9ddd42
• bwa_mem2 was updated to 88bcfaea2fb6
• bwa_mem2 was updated to b4a22d90cce9
• kma was updated to 95ab864b281a
• minimap2 was updated to 11a0d50a54e6

Peak Calling

• ccat was updated to 1a6979fbd544

SAM/BAM

• bamtools was updated to befc9dad4ca8
• bamtools_filter was updated to 1dfd95ee241e
• samtools_calmd was updated to 92ec40abcdcf
• samtools_mpileup was updated to 111f83918fe6
• samtools_mpileup was updated to 329deb17a9f7
• samtools_mpileup was updated to 9da0311ab1dd
• bamtools_split_mapped was updated to 2ed961caae0a
• bamtools_split_paired was updated to 75104ddce35f
• bamtools_split_ref was updated to 09470ab960f1
• bamtools_split_tag was updated to c9fbbe6f5fc8
• samtools_coverage was updated to 90f2dd176d80
• samtools_markdup was updated to 8c440c3002bc
• samtools_merge was updated to b40e2d865d52
• samtools_view was updated to 0dbf49c414ae

HiCExplorer

• hicexplorer_hicfindrestrictionsites was updated to 8823a9d45ed0
• hicexplorer_hicfindrestrictionsites was updated to 9369e9b11b8d

Phylogenetics

• hyphy_absrel was updated to 3f59ebfbfe3d
• hyphy_annotate was updated to 0cd45491b297
• hyphy_annotate was updated to fa913c2975da
• hyphy_busted was updated to d09dd951d0c4
• hyphy_cfel was updated to 0990351232c6
• hyphy_cfel was updated to fcabcc150d21
• hyphy_fel was updated to 09afc9104fc8
• hyphy_fel was updated to fc50c4bac0a3
• hyphy_slac was updated to 0c6724c345d9
• hyphy_slac was updated to 54a5bb259ba2
• hyphy_strike_ambigs was updated to 4bf743518e41
• hyphy_strike_ambigs was updated to dc8875a13914
• nextalign was updated to 1c785a6b4d90
• nextalign was updated to 4771f8bc8fa4
• nextclade was updated to 51f5e7505c4b
• nextclade was updated to d34df92e598f
• pangolin was updated to 36912871ccdc
• pangolin was updated to ca0d8cf80567
• usher was updated to 524cb8f7a69a
• usher was updated to 8f6c7638eab2
• usher_matutils was updated to 52fd1d491417

None

• data_manager_genomic_super_signature_ravmodels was updated to b5bca6d58e4c
• data_manager_humann_database_downloader was updated to 87febc68b45b

Apollo

• apollo_create_account was updated to 0929c15c3d70
• apollo_create_or_update was updated to 9e7b8c7185ad
• apollo_delete_features was updated to 02404029ae4c
• apollo_delete_organism was updated to 3b4fe78bbe83
• apollo_export was updated to c3251541cf2b
• apollo_feat_from_gff3 was updated to 12ebb583b8a3
• apollo_fetch_jbrowse was updated to 654af4ba76bc
• apollo_iframe was updated to 29159d9ce6f0
• apollo_list_organism was updated to 78abc724d792