Commits for jnavarr5

v491_base to v492_preview (2025-11-24 to 2025-12-01) v492

f69a8b38592faaedf9c6f254ce5d56e73d91ac64 Tue Sep 30 10:48:18 2025 -0700

• Initial commit of the customTrack tutorial, refs #34354
  • src/hg/hgCustom/hgCustom.c - lines changed 14, context: html, text, full: html, text
  • src/hg/js/hgCustom.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/tutorials/customTrackTutorial.js - lines changed 71, context: html, text, full: html, text
  • src/hg/js/tutorials/makefile - lines changed 1, context: html, text, full: html, text

ea778c06746a6f023fb1f6e8409a36c073876c38 Fri Oct 31 17:22:53 2025 -0700

• Adding some steps but not done yet
  • src/hg/js/tutorials/customTrackTutorial.js - lines changed 45, context: html, text, full: html, text

89293f440067bbdd4e9473a7a86f5aff761d2b2e Tue Nov 25 14:06:09 2025 -0800

• Updating otto crontab, no Redmine.
  • src/hg/utils/otto/otto.crontab - lines changed 1, context: html, text, full: html, text

aaec16b62487ea4d0a0c19193428917e095c756b Tue Nov 25 14:10:47 2025 -0800

• Updating the clinVarToBed script to match the one the one that is running on dev, no Redmine
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 58, context: html, text, full: html, text

742f49971278e8b13c9d6bfef8be97263eae84d1 Tue Nov 25 16:44:28 2025 -0800

• Updating the pairLastzWrapper.py script so it can generate liftOver files for the older assemblies. Previously, you would get a message saying the assembly was suppressed since it could not determine the clade using the file given (all.*.today), refs #36712 #33200
  • src/utils/qa/pairLastzWrapper.py - lines changed 9, context: html, text, full: html, text

54d2ab3bc67708e54ef4ce54b0bd94927e1ff18b Tue Nov 25 16:57:38 2025 -0800

• Curling the URL like Hiram recommended. Using the file from /hive was not the most up-to-date, refs #36712 #33200
  • src/utils/qa/pairLastzWrapper.py - lines changed 1, context: html, text, full: html, text

984a3761c1300e20e463304a81098b312da7bd66 Wed Nov 26 15:49:51 2025 -0800

• Adding the custom track tutorial, refs #34354
  • src/hg/hgCustom/hgCustom.c - lines changed 18, context: html, text, full: html, text
  • src/hg/js/hgCustom.js - lines changed 17, context: html, text, full: html, text
  • src/hg/js/tutorials/customTrackTutorial.js - lines changed 326, context: html, text, full: html, text
  • src/hg/js/tutorials/tutorialPopup.js - lines changed 21, context: html, text, full: html, text

148452cbb04d1585ca0efb73cff479ccba0ea9d1 Wed Nov 26 16:46:58 2025 -0800

• Making edits based on Lou's feedback, refs #34354
  • src/hg/js/tutorials/customTrackTutorial.js - lines changed 17, context: html, text, full: html, text

e3e6c0f4df0c5b580fb65d02738b92217fcea1dc Mon Dec 1 12:14:41 2025 -0800

• Using the wrong database, hg38, and the tutorial should use hg19, refs #34354
  • src/hg/js/tutorials/tutorialPopup.js - lines changed 4, context: html, text, full: html, text

f5b23e253e246d827101c372a3f70aa778995871 Mon Dec 1 12:26:04 2025 -0800

• Updating the text since this tutorial is only available on hg19, refs #34354
  • src/hg/js/tutorials/tutorialPopup.js - lines changed 1, context: html, text, full: html, text

724b13dc3e31de4c791108908e12925c992d9145 Mon Dec 1 13:05:51 2025 -0800

• Adding the db= parameter to fix a bug if the user clicked the button while viewing a hub, no Redmine.
  • docs/gb101.md - lines changed 1, context: html, text, full: html, text