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