Commits for hiram

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

9d843bd7d7d7c373b47631456f5ee0043f6d2cea Mon May 11 12:01:52 2026 -0700

• otto liftOver tracks are commented out so they will not pollute the hgwdev browser refs #31811
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 3, context: html, text, full: html, text

93026392de53b8abf15a3605b88aa6d7fb0f962d Mon May 11 12:05:53 2026 -0700

• do not need to run "make" in the trackDb since the "include" line is now a comment refs #31811
  • src/hg/utils/otto/userRequests/chainNetTrackDb.pl - lines changed 30, context: html, text, full: html, text

19e534539738dc80225bff27bda1f1835dc5b3d3 Mon May 11 15:09:10 2026 -0700

• rate limit the lifrt requests to "liftDailyLimi" setting from hg.conf refs #31811
  • src/hg/htdocs/liftRequest.html - lines changed 11, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 40, context: html, text, full: html, text
  • src/hg/js/liftRequest.js - lines changed 24, context: html, text, full: html, text

5648ce80fa4b2461fd6ef1d2192370896472cf37 Mon May 11 15:11:22 2026 -0700

• correctly recognize previous lastz/chain/net completed by in-house process and go directly to the hgdownload push and improve the efficiency of the web page ottoRequestView CGI refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 46, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 45, context: html, text, full: html, text

79837f643d9b21431d679ea7216f7e68150b2adf Mon May 11 15:34:40 2026 -0700

• making the ottoRequestView CGI efficient and avoiding repeatedly scanning files to get numbers that are not changing refs #31811
  • src/hg/utils/otto/userRequests/featureBitsSnapshot.py - lines changed 197, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 12, context: html, text, full: html, text

6746944c5c6e9318343c8895d908f444179b70bc Tue May 12 12:44:39 2026 -0700

• beginning of script to add contrib tracks to genark assemblies refs #37543
  • src/hg/utils/otto/genarkContrib/genarkContrib.sh - lines changed 106, context: html, text, full: html, text

e07b87b45f9293c3f45337303886450c390b2585 Tue May 12 13:10:56 2026 -0700

• protect against duplicated pending entries in the ottoRequest table refs #31811
  • src/hg/htdocs/liftRequest.html - lines changed 8, context: html, text, full: html, text
  • src/hg/hubApi/dataApi.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 58, context: html, text, full: html, text
  • src/hg/js/liftRequest.js - lines changed 49, context: html, text, full: html, text

a3b8a28c0a5fe9cd632f43784209a80f42607333 Tue May 12 13:18:19 2026 -0700

• protect against duplicated pending entries in the ottoRequest table refs #31811
  • src/hg/htdocs/style/liftRequest.css - lines changed 20, context: html, text, full: html, text

347a829a0b6a74252991d638a3aa5616197a8069 Wed May 13 13:35:17 2026 -0700

• fix broken anchor link typo error
  • src/hg/hgCollection/hgCollection.c - lines changed 1, context: html, text, full: html, text

d95edf23464d1e0768072f9ed96d6d237ff9da83 Thu May 14 10:41:48 2026 -0700

• push script for any GenArk hub update refs #31811
  • src/hg/utils/otto/userRequests/ottoBuildGenArkHub.py - lines changed 152, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoLib.py - lines changed 212, context: html, text, full: html, text

b949789517a3c519ff77d0763d2175497599d62e Thu May 14 10:51:36 2026 -0700

• fixup the H5N1 name per user bug report
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 2, context: html, text, full: html, text

c3fc03a88ff8fcd8fffadcdd960693268c2a6f5f Thu May 14 11:43:43 2026 -0700

• correctly use a dedicated clean otto kent source tree for operations in the source tree refs #31811
  • src/hg/utils/otto/userRequests/ottoBuildGenArkHub.py - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoLib.py - lines changed 44, context: html, text, full: html, text

9b6653339725825ef07c07651fd3003ac1fd88b6 Fri May 15 12:49:43 2026 -0700

• adding in html description page refs #31811
  • src/hg/makeDb/doc/vgp577way/mkHtml.pl - lines changed 351, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/mkTdb.sh - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/vgp577way.pl - lines changed 238, context: html, text, full: html, text

f3f2f2737fb10c23e74c589ded7a1dae1b6a760b Fri May 15 13:40:09 2026 -0700

• add description page and phyloP track for VGP 577-way refs #31811
  • src/hg/makeDb/trackDb/human/hg38/vgp577way.html - lines changed 748, context: html, text, full: html, text

18a9b36bfd20cd33be49311a62bda0a268ea670b Fri May 15 14:02:29 2026 -0700

• add description page and phyloP track for VGP 577-way refs #31811
  • src/hg/makeDb/trackDb/human/hs1/vgp577way.html - lines changed 748, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/vgp577way.html - lines changed 748, context: html, text, full: html, text

0f8e1c68f7bd3806bfd5c0fe0005ee9b71ffdc92 Fri May 15 14:06:48 2026 -0700

• add description page and phyloP track for VGP 577-way refs #31811
  • src/hg/makeDb/trackDb/human/hg38/vgp577way.trackDb.ra - lines changed 28, context: html, text, full: html, text

6469e916f4e7cd2797e63f1e0943bb2b65764632 Mon May 18 09:59:47 2026 -0700

• empty shell to build out for a liftRequest CGI refs #31811
  • src/hg/liftRequest/liftRequest.c - lines changed 49, context: html, text, full: html, text
  • src/hg/liftRequest/makefile - lines changed 18, context: html, text, full: html, text