Commits for jnavarr5

v354_base to v355_preview (2017-08-28 to 2017-09-04) v355

c4ddd6cf7023dcd804f041d8e37a1821081d85b3 Mon Aug 28 16:40:14 2017 -0700

• Fixing broken links found by the broken link report for oryLat2, no redmine
  • src/hg/makeDb/trackDb/chainNet.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ensGene.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/est.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/genscan.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/intronEst.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/ctgPos2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mrna.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/nestedRepeats.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pubs.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pubsBingBlat.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refGene.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rmsk.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tRNAs.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapTailer.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/windowmaskerSdust.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenoMrna.html - lines changed 9, context: html, text, full: html, text

5dae7b18e9a1d5e6155a982fdc58e0d7a89fbd56 Tue Aug 29 08:56:45 2017 -0700

• Fixing broken links found by the broken link report for melUnd1, no redmine
  • src/hg/makeDb/trackDb/birds/melUnd1/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/melUnd1/gold.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cpgIslandSuper.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ucscToINSDC.html - lines changed 1, context: html, text, full: html, text

42e1ceff3c233348062964c8048dfe137dcf5d94 Tue Aug 29 16:26:28 2017 -0700

• Adding a missing period, CR #20054
  • src/hg/makeDb/trackDb/human/hg38/tcgaExpr.html - lines changed 1, context: html, text, full: html, text

aa095bab8c3a52223ce90941f1aa0c698b890034 Wed Aug 30 09:43:28 2017 -0700

• Fixing broken links found by the broken link report for fr1, no Redmine
  • src/hg/makeDb/trackDb/blastHg17KG.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/blatHg16.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/ecoresHg16.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/ecoresRn3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/ensGene.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/est.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr1/genomicSuperDups.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/gap.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/intronEst.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/mrna.html - lines changed 6, context: html, text, full: html, text

14ee20d3658462756bda2cf82463389032930702 Thu Aug 31 09:47:13 2017 -0700

• Fixing broken links found by the broken link report for felCat3, no Redmine
  • src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ensemblGeneScaffold.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/geneid.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/nscanGene.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMap.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnMRna.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnRefSeq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnSplicedEst.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnUcscGenes.html - lines changed 6, context: html, text, full: html, text

f1f8d705c60c02d1c66a32f26ab7d334cf338d6f Thu Aug 31 10:32:01 2017 -0700

• Adding a link to the Toil home page, refs #19350
  • src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html - lines changed 4, context: html, text, full: html, text

1c3a1fba24adfb8092672478fa99ced539d125c4 Thu Aug 31 10:49:06 2017 -0700

• Replacing single quotes with double quotes for HTML attributes, refs #19350
  • src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html - lines changed 3, context: html, text, full: html, text

0a9933520f41643aef5ee2f5eb7eed00d5fa3e7b Thu Aug 31 11:13:43 2017 -0700

• Adding spacing to the barchart image, refs #19350
  • src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html - lines changed 2, context: html, text, full: html, text

989ab541a5249d80d2625247880a0fd22f38cd6a Thu Aug 31 11:29:03 2017 -0700

• Italicizing our tools, refs #19350
  • src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html - lines changed 4, context: html, text, full: html, text

a22be5d8fb33bbb0f91a315694f4ee29767e2f0e Thu Aug 31 11:57:41 2017 -0700

• Updating broken and redirected links, refs #19350
  • src/hg/makeDb/trackDb/human/hg38/gtexTranscExpr.html - lines changed 17, context: html, text, full: html, text

93d5103daee27501d0aad87753ac52f69ceba551 Thu Aug 31 16:02:46 2017 -0700

• Adding a maxItems limit to prevent loading issues, refs #19350
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 1, context: html, text, full: html, text

4c5fc8b9a459abc9bc3cef56e88e4748446010a0 Fri Sep 1 08:20:28 2017 -0700

• Fixing redirected links found by the broken link report for nomLeu1, no Redmine
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html - lines changed 1, context: html, text, full: html, text

426897afe49d05e59bac35a5d630352a8a3fe459 Fri Sep 1 11:26:46 2017 -0700

• Creating a shared HTML page for the GTEx Transcript track on hg19. Adding a note about how the coordinates were converted from hg38 to hg19. refs #19350
  • src/hg/makeDb/trackDb/human/hg19/gtexTranscExpr.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text

bb3e4008901303e6ad9c131380ede5cfdd2c9c37 Fri Sep 1 15:10:00 2017 -0700

• Adding the beta release tag to stage the GTEx Transcript Expression on hgwbeta, refs #19350
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 1, context: html, text, full: html, text