Commits for hiram

v499_preview2 to v499_base (2026-05-25 to 2026-06-01) v499

2fb68bdc7e7512791f7dfa748dc659c59bed62cb Tue May 26 20:12:50 2026 -0700

• cleanup and make MAF download files refs #31811
  • src/hg/makeDb/doc/vgp577way/vgp577way.txt - lines changed 45, context: html, text, full: html, text

375022845a4226d17c2717cc844f4e3ef5eb5b5e Tue May 26 20:13:31 2026 -0700

• resetting the bigDataUrl to hgdownload addresses refs #31811
  • src/hg/makeDb/doc/vgp577way/vgp577way.pl - lines changed 7, context: html, text, full: html, text

e8f2620df2a833ef15bdc2c7c4e132302770c900 Tue May 26 20:14:28 2026 -0700

• now have data access on hgdownload refs #31811
  • src/hg/makeDb/doc/vgp577way/mkHtml.pl - lines changed 39, context: html, text, full: html, text

855cad962a8fc6abc4a053c7a4575b263fa864d3 Wed May 27 14:45:12 2026 -0700

• correctly use the hg.conf settings and correct bounce email, can now monitor both hgwdev and the RR hgcentral table refs #31811
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 19, context: html, text, full: html, text

b56beb6914a7522fc2b92b0de951dc6ca7de8e28 Wed May 27 14:50:42 2026 -0700

• otto cron script to monitor both hgwdev and RR ottoRequest table in hgcentral refs #31811
  • src/hg/utils/otto/userRequests/devAndRR.sh - lines changed 18, context: html, text, full: html, text

bf5d4df9d70cd73ff59379ccb2f16d545ccc00f8 Wed May 27 14:52:56 2026 -0700

• change ottoRequest.py to devAndRR.sh to watch both hgwdev and RR ottoRequest tables refs #31811
  • src/hg/utils/otto/otto.crontab - lines changed 1, context: html, text, full: html, text

348d17775ccde5f178d2b87915f16beda576f8fa Wed May 27 15:29:13 2026 -0700

• add toggle buttons to hide/show the requestType assembly or liftRequest and allow viewing either hgwdev or the RR table refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 113, context: html, text, full: html, text

416fd852b3e64e76d1c4484db14cddbe7e4e635f Wed May 27 15:55:08 2026 -0700

• adding a mailViaPipe function with bounce email address no redmine
  • src/lib/mailViaPipe.c - lines changed 18, context: html, text, full: html, text

45014fb713fc38c6fa2c5ca8e76874c5b48d133d Wed May 27 16:05:11 2026 -0700

• correctly use the appropriate host for the hgcentral table refs #31811
  • src/hg/hubApi/apiUtils.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hubApi/dataApi.h - lines changed 6, context: html, text, full: html, text
  • src/hg/hubApi/findGenome.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 27, context: html, text, full: html, text

80c1747b01eae6af733f106086b95725852bad0a Wed May 27 16:06:46 2026 -0700

• try using the sendmail with correct bounce address no redmine
  • src/hg/hgLogin/hgLogin.c - lines changed 4, context: html, text, full: html, text

043e1c69c0607fdd8a5c09436cfe639823ffb347 Wed May 27 16:10:55 2026 -0700

• adding mailViaPipeBounce function no redmine
  • src/inc/mailViaPipe.h - lines changed 2, context: html, text, full: html, text

52990d0eb995b59123d54fb08898305463095b0e Thu May 28 12:27:22 2026 -0700

• change bounce address refs #31811
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 1, context: html, text, full: html, text

68449d8c910e343a6dbf4b14618050a47437ffd6 Fri May 29 09:28:11 2026 -0700

• fix incorrect path name to hgTrackDb refs #31811
  • src/hg/makeDb/trackDb/loadTracks - lines changed 1, context: html, text, full: html, text

2850f990218910e874ee2abf16fec9dc16d75e0e Mon Jun 1 08:14:03 2026 -0700

• using bounce email correctly refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 11, context: html, text, full: html, text

65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700

• switching entirely to genome-centdb hgcentral refs #31811
  • src/hg/utils/otto/userRequests/kegAlignLastz.sh - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoLib.py - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 6, context: html, text, full: html, text

83956ac6781412699ebf11bfb2fd87cd1833ca87 Mon Jun 1 09:59:44 2026 -0700

• adding one per user request refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text