Commits for hiram

v327_preview to v327_preview2 (2015-12-14 to 2016-01-04) v327

• adding selfChainPileUps and NCBI Gene tracks
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/selfChainPileUps.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 28, context: html, text, full: html, text
• for some odd reason the gene names are not showing on ncbiGene refs no redmine
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• catching build procedure up to date refs #16535
  
  • src/hg/makeDb/doc/oxyTri2/initialBuild.txt - lines changed 604, context: html, text, full: html, text
• adding sequences track refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/sequences.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 25, context: html, text, full: html, text
• adding tracks from Zahler browser ncRNAs microGenes and mergeJunctions refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 27, context: html, text, full: html, text
• add pileUps200 location track and mergeJunctions should be in regulation group refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding BAM file tracks refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/rnaSeq.ra - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• adding felCat8 chain net tracks for hg38 and canFam3 refs #14412
  
  • src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetFelCat8.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 51, context: html, text, full: html, text
• adding coverage bigWig tracks refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/coverage.ra - lines changed 100, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• convert ncbiGenes genePred to xNcbiGenes bed track refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 19, context: html, text, full: html, text
• turning off default name display refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/rnaSeq.ra - lines changed 1, context: html, text, full: html, text
• setting default viz refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/coverage.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/rnaSeq.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 4, context: html, text, full: html, text
• *ncbiGene has become genbankGenes with correct indexes refs #16535
  
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra - lines changed 5, context: html, text, full: html, text
• up to date with current versions now working on both refseq and genbank hierarchies refs #16078
  
  • src/hg/utils/automation/genbank/assemblyDescription.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/buildStats.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/cpg.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gapDescription.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gatewayPage.pl - lines changed 144, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/gc5Description.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiGeneDescription.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ncbiToUcsc.sh - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ucscAltNames.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/ucscPatchNames.sh - lines changed 1, context: html, text, full: html, text
• adding hub construction scripts refs #16078
  
  • src/hg/utils/automation/genbank/hubHtml.pl - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/hubIndexInclude.sh - lines changed 138, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/mkGenomesTxt.sh - lines changed 156, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/mkHubIndex.sh - lines changed 135, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/mkPartitionedGenomes.txt.sh - lines changed 223, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/mkPartitionedHubIndexInclude.sh - lines changed 111, context: html, text, full: html, text
• expanding the README file and adding the hub file layout construction scripts
  
  • src/hg/utils/automation/genbank/README.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/cronUpdate.sh - lines changed 45, context: html, text, full: html, text