v364

Code changes:

• The automation tool chain doBlastzChainNet.pl fixed up to function outside UCSC environment with usage documented in genomewiki: http://genomewiki.ucsc.edu/index.php/DoChainNetBlastz.pl (#18874). Hiram
• The automation tool chain doSameSpeciesLiftOver.pl fixed up to function outside UCSC environment (#18874). Hiram
• hgVai: Angie
  • HGVS output options for GENCODE; use variantProjector for genePreds too (#21142)
  • intergenic row might be no_sequence_variation; use correct SO term (#21204)
  • Watch out for symbolic alleles when converting rs IDs to variant input (#21142)
  • Preserve warnings from initial conversion of rs IDs or HGVS to variant input
• hgTracks: resolve baseColor settings from view with both PSL and genePred (#21194) Angie
• hgTables: handle lack of vcfFileName for some chroms; explainWhyNoResults for vcf out (#21218) Angie
• Improvement to the Genome Browser home icon, should now blend better with other background menu colors. Jonathan
• The DECIPHER otto pipeline has been given better success/failure reporting (#18151). Jonathan
• Added missing CIRM cdwQaAgent script used by pipeline for validation and added missing CIRM cdwCreateGroup to makefile and fixed CIRM bug caused by race condition fix and improved CIRM initialization scripts. Galt Fix where a need to set limitedVis consistently across all windows after loading tracks for multi-region modes (#21267). Galt.
• Continuing development of interact and bigInteract track types. Response to QA issues. Expanded track schemas to include strand for endpoints (request of B Raney and D Zerbino) and added Postscript support for curve drawing (PDF view) (#21109). Kate

Data changes:

• New assemblies. Hiram
  1. New ponAbe3/Orangutan browser QA Ready (#20980)
  2. New panTro6/Chimp browser QA Ready (#20979)
• Open Stack parasol installation scripts in source tree usage documented in genomewiki: (#18874) Hiram
  • http://genomewiki.ucsc.edu/index.php/Open_Stack_Parasol_Installation
  • http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system