kb_phylgenomics 1.9.0

This is the current beta version of this module in KBase.

What's Changed

• restoring Homolog Genome Context App and stub code for Build Species Tree App by @dcchivian in #199
• handle case in find_homologs_in_genome_context() where genome doesn't… by @dcchivian in #200
• fixing errors by @dcchivian in #201
• added localize_DomainAnnotation() App by @dcchivian in #202
• typo by @dcchivian in #203
• adding Genome and Assembly copy to Localize DomainAnnotation by @dcchivian in #204
• lil bug by @dcchivian in #205
• remove input_ws_objects from provenance in case that's causing the tr… by @dcchivian in #206
• playing with dfuClient for save_objects by @dcchivian in #207
• switching all save_objects in localize_DomainAnnotations() to dfu by @dcchivian in #208
• removed meta and provenance from dfu.save_objects() by @dcchivian in #209
• build_microbial_speciestree() can't be tested command line because SpeciesTreeBuilder subcall fails by @dcchivian in #210
• forgot some build_microbial_speciestree() widget code by @dcchivian in #211
• missed some client libs by @dcchivian in #212
• input field is input_genome_refs by @dcchivian in #213
• debugging by @dcchivian in #214
• debugging by @dcchivian in #215
• debugging by @dcchivian in #216
• add in skeleton genomes by @dcchivian in #217
• call trim_speciestree_to_genomeset() in build_microbial_speciestree() by @dcchivian in #218
• adding genome categories to pass through to view_tree() by @dcchivian in #219
• adding colors to leaves in build_microbial_speciestree() by @dcchivian in #220
• skeleton genome info config by @dcchivian in #221
• ws_ref is substructure by @dcchivian in #222
• added label logic by @dcchivian in #223
• debugging by @dcchivian in #224
• debugging by @dcchivian in #225
• debugging by @dcchivian in #226
• debugging by @dcchivian in #227
• debugging by @dcchivian in #228
• completed Phylogenetic Skeleton genomes by @dcchivian in #229
• updated object IDs for RAST-annotated genomes for missing pegs by @dcchivian in #230
• typo for skeleton labels by @dcchivian in #231
• updates to handle exceptional case in PUBLIC-739 by @dcchivian in #232
• forgot to update version in App name by @dcchivian in #233
• added query_2 options by @dcchivian in #234
• try coloring branch by @dcchivian in #235
• handle missing desc for tree_in by @dcchivian in #236
• changed run_DomainAnnotation_Sets() to use beta DomainAnnotation for Pfam32 by @dcchivian in #237
• updated Pfam to v32.0 and added build_gene_tree() method by @dcchivian in #239
• fixed VFP spec.json typo by @dcchivian in #240
• part way through mods for v1.6.0 by @dcchivian in #241
• debugging trim_speciestree_to_genomeset() by @dcchivian in #242
• workspace consistency error messages by @dcchivian in #243
• need to join array by @dcchivian in #244
• hid Build_Strain_Tree() and Build_Pangenome_SpeciesTree() and RefSeq args from Build_Microbial_SpeciesTree() by @dcchivian in #245
• needed to make NONE an explicit string option for Build_Microbial_SpeciesTree() input widget by @dcchivian in #246
• don't pass reference genomes options or tree_shape by @dcchivian in #247
• checkpoint commit to give JMC registration access by @dcchivian in #248
• Fixed spelling of client library by @jmchandonia in #249
• fixed DomainAnnotation_Sets() unit tests by @dcchivian in #250
• parallelize run_DomainAnnotationSets by @jmchandonia in #251
• Fix kb_parallel crash where all genomes already done, and explicitly use library with Pfam 32 by @jmchandonia in #252
• Made DomainAnnotation_Sets run remotely and pass genome_disp from GeneTree to MUSCLE by @dcchivian in #253
• hide inactive Apps by @dcchivian in #254
• v1.7.2 - begin changes by @dcchivian in #255
• merge in old code improvements by @dcchivian in #257

Full Changelog: 1.4.0...1.9.0

kb_phylgenomics 1.4.0

A KBase module for comparative and phylogenomic visualization analysis

What's Changed

• Added unit test for run_DomainAnnotation_Sets by @jmchandonia in #1
• Fixed local call to GeneDomains client by @jmchandonia in #2
• Support for auth2 by @rsutormin in #3
• adding unit tests by @dcchivian in #4
• playing with scaling for pan_circle_plot() by @dcchivian in #5
• playing with scaling for pan_circle_plot() by @dcchivian in #6
• playing with scaling for pan_circle_plot() by @dcchivian in #7
• playing with scaling for pan_circle_plot() by @dcchivian in #8
• playing with scaling for pan_circle_plot() by @dcchivian in #9
• playing with scaling for pan_circle_plot() by @dcchivian in #10
• playing with scaling for pan_circle_plot() by @dcchivian in #11
• playing with pan_circle_plot() scaling by @dcchivian in #12
• playing with scaling for pan_circle_plot() by @dcchivian in #13
• playing with scaling for pan_circle_plot() by @dcchivian in #14
• scaling by @dcchivian in #15
• scaling by @dcchivian in #16
• fix pg_obj name to use actual object name instead of internally store… by @dcchivian in #17
• playing with scaling for pan_circle_plot() by @dcchivian in #18
• playing with scaling for pan_circle_plot() by @dcchivian in #19
• scaling by @dcchivian in #20
• reverse rings to put base genome on outside by @dcchivian in #21
• playing with scaling for pan_circle_plot() by @dcchivian in #22
• playing with scaling for pan_circle_plot() by @dcchivian in #23
• playing with scaling for pan_circle_plot() by @dcchivian in #24
• playing with scaling for pan_circle_plot() by @dcchivian in #25
• scaling by @dcchivian in #26
• playing with scaling for pan_circle_plot() by @dcchivian in #27
• playing with scaling for pan_circle_plot() by @dcchivian in #28
• playing with scaling for pan_circle_plot() by @dcchivian in #29
• playing with scaling for pan_circle_plot() by @dcchivian in #30
• playing with scaling for pan_circle_plot() by @dcchivian in #31
• playing with scaling for pan_circle_plot() by @dcchivian in #32
• playing with scaling for pan_circle_plot() by @dcchivian in #33
• playing with scaling for pan_circle_plot() by @dcchivian in #34
• playing with scaling for pan_circle_plot() by @dcchivian in #35
• playing with scaling for pan_circle_plot() by @dcchivian in #36
• playing with scaling for pan_circle_plot() by @dcchivian in #37
• think I'm done playing with scaling for pan_circle_plot() by @dcchivian in #38
• fix space in obj name by @dcchivian in #39
• remove featureSet element delimiter by @dcchivian in #40
• FeatureSet ids fixed (addresses PUBLIC-215) by @dcchivian in #41
• bumped version to 1.0.1 for view_pan_circle_plot() by @dcchivian in #42
• adding view_tree() by @dcchivian in #43
• bumped versions by @dcchivian in #44
• link App to correct method by @dcchivian in #45
• debugging newick_buf by @dcchivian in #46
• just get rid of problematic (kb|g.1234) part of labels by @dcchivian in #47
• debugging by @dcchivian in #48
• debugging by @dcchivian in #49
• debugging by @dcchivian in #50
• debugging by @dcchivian in #51
• remove debugging by @dcchivian in #52
• make parens brackets instead of hex escape by @dcchivian in #53
• workflow thumbnails by @dcchivian in #54
• resize thumbnails by @dcchivian in #55
• save featuresets from pangenome dissection in view_pan_phylo() by @dcchivian in #56
• tidy up by @dcchivian in #57
• fixing node ids in view_pan_phylo() by @dcchivian in #58
• fix all instances of keys().sort() by @dcchivian in #59
• fixed pangenome obj name setting in view_pan_phylo() by @dcchivian in #60
• typo by @dcchivian in #61
• add logging to debug by @dcchivian in #62
• fix sort of node_num_ids in view_pan_phylo() by @dcchivian in #63
• Fixes for kbReports by @JamesJeffryes in #64
• Highlight user genome in species tree by @JamesJeffryes in #65
• Bump version and revert test changes by @JamesJeffryes in #66
• fix for PTV-1133 / PUBLIC-491 (read 'functions' field in features for Genome-9.0) by @dcchivian in #67
• update version for input widgets by @dcchivian in #68
• fixed version for View_Tree() by @dcchivian in #69
• updated citations and patch by @mclark58 in #71
• Citations for Annotate Domains in a GenomeSet by @mclark58 in #72
• Adding KBase Publication to display.yaml by @thebenallen in #70
• adding find_homologs_with_genome_context() method. dev version 1 by @dcchivian in #73
• debugging by @dcchivian in #74
• fixing table structure and tree row order by @dcchivian in #75
• get leaf ids before replaced by labels by @dcchivian in #76
• typo-level bug by @dcchivian in #77
• getting punchy and making stupid mistakes by @dcchivian in #78
• adjust height of tree and add bait gene header row by @dcchivian in #79
• playing with tree height scaling by @dcchivian in #80
• more playing with tree height scaling by @dcchivian in #81
• rescaling tree by @dcchivian in #82
• fixed typo and more tweaks by @dcchivian in #83
• fixed typo, adding spacing to hit table by @dcchivian in #84
• restored missing var by @dcchivian in #85
• playing with table by @dcchivian in #86
• fix misining key by @dcchivian in #87
• getting punchy by @dcchivian in #88
• playing with tree image by @dcchivian in #89
• trying to fix species tree in html report by @dcchivian in #90
• debugging by @dcchivian in #91
• adding neighbor_thresh option (inactive so far) and fixing gen...