UseGalaxy.eu Tool Updates for 2021-01-26

January 26, 2021

Multiple Alignments
Variant Calling
RNA Analysis
Assembly
Mapping
Annotation
SAM/BAM
Data Managers
Graph/Display Data
Mothur
Phylogenetics
Proteomics
Convert Formats
hca_sc_utils_viz
hca_sc_get-scrna
hca_sc_seurat_tools
hca_sc_label_analysis_tools
Species abundance

On 2021-01-26, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #256

Multiple Alignments

chromeister was updated to a6d1f83c46b4

Variant Calling

delly_call was updated to 9946bd542898
delly_classify was updated to d3bc6ec7881f
delly_cnv was updated to d402af96808e
delly_filter was updated to 6184cfc70e28
delly_lr was updated to ceda4714f3a1
delly_merge was updated to 148389992630
sansa_annotate was updated to fb00426402b0
vcfanno was updated to fb20fa735dfe

RNA Analysis

ruvseq was updated to fed9d0350d72

Assembly

salsa was updated to 575b4d5bd444
metaspades was updated to 01a241476407
metaspades was updated to 2ecf5a570907

Mapping

bowtie2 was updated to 09b2cdb7ace5
hisat2 was updated to 26371a1df031
rgrnastar was updated to 7ed2edc1337f
rna_starsolo was updated to ec9cbd6b9a49

Annotation

hmmer_alimask was updated to 92227c141aa5
hmmer_hmmalign was updated to d430c68061f7
hmmer_hmmbuild was updated to 6846f8789e33
hmmer_hmmconvert was updated to 649b289b4ccc
hmmer_hmmemit was updated to a6f41287ef2b
hmmer_hmmfetch was updated to 01c842e297f5
hmmer_hmmscan was updated to d92dd2f040cd
hmmer_hmmsearch was updated to 192a5046d9a2
hmmer_jackhmmer was updated to d9ce554da9b4
hmmer_nhmmer was updated to 314b778b8ffa
hmmer_nhmmscan was updated to 24a67ef302dd
hmmer_phmmer was updated to 8267b6ad0b45
maker was updated to 5201ec38c01f
maker was updated to d46d803ca6cc
maker_map_ids was updated to e408aa831db3

SAM/BAM

pileup_interval was updated to 9c1c0b947e46

Data Managers

data_manager_build_kma_index was updated to 2c532a6eee3f

Graph/Display Data

bandage was updated to 94fe43e75ddc

Mothur

mothur_align_check was updated to 0399e5aeaac6
mothur_align_check was updated to 2f668a63a256
mothur_align_seqs was updated to 02ba09e31d94
mothur_align_seqs was updated to abf7c15ecfef
mothur_amova was updated to 58b8ae43d27f
mothur_anosim was updated to 4a283edb151c
mothur_bin_seqs was updated to 3fc101a0498f
mothur_bin_seqs was updated to 65000a433c3b
mothur_chimera_bellerophon was updated to 14a7c1eca23d
mothur_chimera_ccode was updated to 6e2e58e07e0f
mothur_chimera_ccode was updated to 751904c1033d
mothur_chimera_check was updated to 4b57c3241cbc
mothur_chimera_check was updated to 74dfe7be1563
mothur_chimera_perseus was updated to 0f3baac24045
mothur_chimera_perseus was updated to 6db50600493e
mothur_chimera_pintail was updated to 2960e484721c
mothur_chimera_pintail was updated to 5f66e6f7f6c0
mothur_chimera_slayer was updated to 753321ddded9
mothur_chimera_slayer was updated to ab328c924a02
mothur_chimera_uchime was updated to 0706d327ecae
mothur_chop_seqs was updated to 29f963e785a0
mothur_chop_seqs was updated to e1dd67d13282
mothur_classify_otu was updated to 02446d12c359
mothur_classify_seqs was updated to 09bf9e496c64
mothur_classify_tree was updated to 5d8809423177
mothur_clearcut was updated to 20e764494303
mothur_clearcut was updated to ad924a6328cc
mothur_cluster was updated to 3bb756df109c
mothur_cluster was updated to 528f950d1044
mothur_cluster_classic was updated to 14e978a6ffdf
mothur_cluster_classic was updated to 9bae6b20ed44
mothur_cluster_fragments was updated to 08b0e9f01d65
mothur_cluster_split was updated to 1b7fd1678230
mothur_collect_shared was updated to 21a043c3ae00
mothur_collect_single was updated to 9ee1a391ed43
mothur_collect_single was updated to c9d3eed082fc
mothur_consensus_seqs was updated to 6f281dc9d01c
mothur_cooccurrence was updated to 0e05f58541d0
mothur_cooccurrence was updated to ffdcb7942343
mothur_corr_axes was updated to 03b02c255008
mothur_count_groups was updated to 03c86648a52e
mothur_count_seqs was updated to 59a962f57cb5
mothur_count_seqs was updated to 7a6f9c899221
mothur_create_database was updated to 16f6d606521a
mothur_degap_seqs was updated to 104cea550c2f
mothur_degap_seqs was updated to 6f08af23888a
mothur_deunique_seqs was updated to 0369aff1be76
mothur_deunique_seqs was updated to f6c604b2793e
mothur_deunique_tree was updated to 2b96ca0b44c0
mothur_deunique_tree was updated to d247213cebfc
mothur_dist_seqs was updated to 0554c9338ca0
mothur_dist_shared was updated to 1a899fec55e1
mothur_dist_shared was updated to f25598da7174
mothur_fastq_info was updated to 1edab4936153
mothur_fastq_info was updated to a630c5167f5d
mothur_filter_seqs was updated to 3524ca06478e
mothur_filter_shared was updated to 007311ce6297
mothur_filter_shared was updated to 2d1dbf69f589
mothur_get_communitytype was updated to 10c5aa12a1d5
mothur_get_coremicrobiome was updated to 42244e3619cf
mothur_get_coremicrobiome was updated to da05ce41f8f0
mothur_get_dists was updated to 10005fd5ad53
mothur_get_group was updated to 081d0fbf9751
mothur_get_group was updated to 65d9f4688890
mothur_get_groups was updated to 03af14e245fb
mothur_get_label was updated to 78e5065b27bd
mothur_get_label was updated to ee13e5a4f9f3
mothur_get_lineage was updated to 0bbfc05d924e
mothur_get_mimarkspackage was updated to 2d19319f528a
mothur_get_otulabels was updated to 78168125a0c0
mothur_get_otulabels was updated to fbd1d5bf02bf
mothur_get_otulist was updated to 2478fb777d97
mothur_get_otulist was updated to 85f75125d861
mothur_get_oturep was updated to 305ce07a4b16
mothur_get_otus was updated to 278a9f09614c
mothur_get_otus was updated to dbb1bc225df1
mothur_get_rabund was updated to 08a740b388d8
mothur_get_rabund was updated to 4a52424269e1
mothur_get_relabund was updated to 1593a3542944
mothur_get_sabund was updated to 0bc1dc0c6aad
mothur_get_sabund was updated to c550ce2ebe1f
mothur_get_seqs was updated to 32a95d4cd850
mothur_get_seqs was updated to f5cb275acba9
mothur_get_sharedseqs was updated to 32040fb8ffdf
mothur_get_sharedseqs was updated to f8bf3dd4db47
mothur_heatmap_bin was updated to 416182d7281c
mothur_heatmap_bin was updated to aeacbc9d5333
mothur_heatmap_sim was updated to 0674bdcb3019
mothur_heatmap_sim was updated to 7f5707dd6073
mothur_homova was updated to 68005ede9e6e
mothur_homova was updated to 89054fe2207f
mothur_indicator was updated to 0232e2fe594c
mothur_indicator was updated to 1c6dadf7bc72
mothur_lefse was updated to 7691a4b846fc
mothur_lefse was updated to ccd1ce71c11f
mothur_libshuff was updated to 1cd0f3241d5b
mothur_list_otulabels was updated to 0c9eb32683bf
mothur_list_otulabels was updated to 1c8906cc1ddd
mothur_list_seqs was updated to 0ad4a88e6314
mothur_list_seqs was updated to dd84878a5f99
mothur_make_biom was updated to 143cd841de28
mothur_make_biom was updated to 55e975c9a012
mothur_make_contigs was updated to 4e9136c2c4c3
mothur_make_design was updated to 185c17f84d91
mothur_make_design was updated to 6ec3ec95ae68
mothur_make_fastq was updated to 1684157db3c1
mothur_make_fastq was updated to f09c0a3bf8b9
mothur_make_group was updated to 182b471ed56b
mothur_make_group was updated to 37af7f0540e5
mothur_make_lefse was updated to 2da52b4bf3dc
mothur_make_lefse was updated to 470c067fc0a0
mothur_make_lookup was updated to 23c1af22331b
mothur_make_shared was updated to 0851ae17c58e
mothur_make_sra was updated to 2341a1066c67
mothur_make_sra was updated to 88fa82b36a72
mothur_mantel was updated to 17b471efdc40
mothur_mantel was updated to b0f1e033e18d
mothur_merge_files was updated to 129646af86bc
mothur_merge_files was updated to 7bd37d6decd9
mothur_merge_groups was updated to 052bc33e134e
mothur_merge_groups was updated to ddd068a49efe
mothur_merge_sfffiles was updated to 0778c4b6a300
mothur_merge_sfffiles was updated to b562d71b9508
mothur_merge_taxsummary was updated to 3a2ee62cb710
mothur_merge_taxsummary was updated to 733bfc5872b1
mothur_metastats was updated to 19836a38dc20
mothur_mimarks_attributes was updated to 247d1bacbefe
mothur_mimarks_attributes was updated to b9fe5cf8f2bc
mothur_nmds was updated to 3cc04a065490
mothur_nmds was updated to a81680d1db78
mothur_normalize_shared was updated to 4bdf28c910af
mothur_normalize_shared was updated to 5e94c135ef00
mothur_otu_association was updated to 12af8c375bb8
mothur_otu_association was updated to a02117aa58a5
mothur_otu_hierarchy was updated to 0161571cd8f8
mothur_otu_hierarchy was updated to f9326e93f5c3
mothur_pairwise_seqs was updated to 39c7213ca279
mothur_pairwise_seqs was updated to cfe04aa12a39
mothur_parse_list was updated to 408650f291f7
mothur_parsimony was updated to 65955ae23f29
mothur_parsimony was updated to aff64115d95f
mothur_pca was updated to 46689a444f2b
mothur_pcoa was updated to 1c1d69d94f7d
mothur_pcoa was updated to 5bc3e30e1d9e
mothur_pcr_seqs was updated to 0a23bfe005be
mothur_pcr_seqs was updated to 7dba7376870c
mothur_phylo_diversity was updated to c76d9ea84d39
mothur_phylotype was updated to 249cdeb3cdb1
mothur_phylotype was updated to 4d219b4dfd6a
mothur_pre_cluster was updated to 05183ee20cf8
mothur_primer_design was updated to 0b63f5faf6e5
mothur_rarefaction_shared was updated to 2175b62675ed
mothur_rarefaction_single was updated to 57e3e6bf2e41
mothur_rarefaction_single was updated to af521db77c56
mothur_remove_dists was updated to 11795a719c90
mothur_remove_dists was updated to 56ad298415d8
mothur_remove_groups was updated to 2d5258c52be0
mothur_remove_groups was updated to 498dc0671d9e
mothur_remove_lineage was updated to 2a4d6c3d9b6d
mothur_remove_lineage was updated to 947faa8b3205
mothur_remove_otulabels was updated to 2cbf56d15f4b
mothur_remove_otulabels was updated to b9e2724e9fc7
mothur_remove_otus was updated to 0e73681a7cdc
mothur_remove_rare was updated to 196b1583580a
mothur_remove_rare was updated to 9ac808d4e0b5
mothur_remove_seqs was updated to 2fa446f85b18
mothur_remove_seqs was updated to 5097ac2cbfc3
mothur_reverse_seqs was updated to 03450507aa98
mothur_reverse_seqs was updated to 7378ce8fb5c1
mothur_screen_seqs was updated to 63b74bfc8052
mothur_sens_spec was updated to 084dc4e8caae
mothur_sens_spec was updated to 5ff10ccd7100
mothur_seq_error was updated to 2851c368b879
mothur_seq_error was updated to 5a7674ac2c59
mothur_sffinfo was updated to 09e3b0966a11
mothur_shhh_flows was updated to 408595fde5c6
mothur_shhh_flows was updated to dfaf60f40e94
mothur_shhh_seqs was updated to 151a711dec84
mothur_shhh_seqs was updated to d7e469b059da
mothur_sort_seqs was updated to 2f6a9498447e
mothur_sort_seqs was updated to fc60d2e290a4
mothur_split_abund was updated to 3a364dd93195
mothur_split_abund was updated to cd7b11709aa9
mothur_split_groups was updated to 618bf5d295e7
mothur_sub_sample was updated to 0f4dfa0332e8
mothur_sub_sample was updated to 67cb43432196
mothur_summary_qual was updated to 11be0e5f3ebb
mothur_summary_qual was updated to 86a40294e149
mothur_summary_seqs was updated to 1a8e53763086
mothur_summary_seqs was updated to 609770e516fa
mothur_summary_shared was updated to 47370a4efc95
mothur_summary_shared was updated to 545234c1d925
mothur_summary_single was updated to 2344ed181ae6
mothur_summary_tax was updated to 4db7f1329d0e
mothur_summary_tax was updated to a7e1d78c70f5
mothur_tree_shared was updated to 43e2715e98c9
mothur_trim_flows was updated to 1fead600dbd4
mothur_trim_seqs was updated to 29dfb8d90999
mothur_trim_seqs was updated to bf67e22a405f
mothur_unifrac_unweighted was updated to 2933ee6251d8
mothur_unifrac_weighted was updated to 20bc6be9e1df
mothur_unifrac_weighted was updated to 88c441e56578
mothur_unique_seqs was updated to 7c3f9c0850ac
mothur_unique_seqs was updated to d466580cd706
mothur_venn was updated to 200defe4c42b
mothur_venn was updated to 4db54b1c1d83

Phylogenetics

t_coffee was updated to ae69d14b6fbf
hyphy_absrel was updated to 3b8b5bde0bd9
hyphy_absrel was updated to b89cac5156ec
hyphy_bgm was updated to 082d47606949
hyphy_bgm was updated to cebcce34d63b
hyphy_busted was updated to 2228dcc23dd9
hyphy_busted was updated to 6acfd47732d1
hyphy_fade was updated to 29515b569f8b
hyphy_fade was updated to 751948c21000
hyphy_fel was updated to ccf8f1712632
hyphy_fubar was updated to 80c9e5256a0d
hyphy_fubar was updated to af40a8b95f8d
hyphy_gard was updated to 6a726db04d4b
hyphy_gard was updated to a185b079b095
hyphy_meme was updated to a4bf56abff97
hyphy_meme was updated to d9dc61719379
hyphy_prime was updated to 76f42c7f9b7b
hyphy_prime was updated to a8f760e7c322
hyphy_relax was updated to 169f4d983656
hyphy_relax was updated to 63f85ef1a3d5
hyphy_slac was updated to 08449da86cdf
hyphy_slac was updated to ae4e61b62996
hyphy_sm19 was updated to 051642420aec
hyphy_sm19 was updated to 466217f0aa76

Proteomics

msstatstmt was updated to fd3dc69b78ff
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
peptideshaker was updated to 1beff3ddce58

Convert Formats

gffcompare_to_bed was updated to ba5368c19dbd

hca_sc_utils_viz

dropletutils_empty_drops was updated to fa662ca7ae7f
dropletutils_read_10x was updated to ca62f52e0d7f

hca_sc_get-scrna

hca_matrix_downloader was updated to c3c85b67d118

hca_sc_seurat_tools

seurat_run_tsne was updated to 2d294978b152

hca_sc_label_analysis_tools

ct_build_cell_ontology_dict was updated to 512b239a11ad
ct_combine_tool_outputs was updated to 844689a7f66e
ct_get_consensus_outputs was updated to 0917f5e09d83
ct_get_empirical_dist was updated to 14eb5128af69

Species abundance

stoc_mainglm was updated to a961be0a964f
stoc_mainglm_group was updated to 8f953c35c787