Commits for hiram

v498_preview2 to v498_base (2026-05-04 to 2026-05-11) v498

7a4080b1727435d2c348f5d672823d80411eb1d6 Mon May 4 15:01:47 2026 -0700

• fix hgc click on mafWig track when GCx accessions are in use with speciesLabels
  • src/hg/hgc/mafClick.c - lines changed 30, context: html, text, full: html, text

0a05f3e3c58ea53afa036c0d0be18d4eb79e11b5 Mon May 4 15:28:20 2026 -0700

• enable B links for maf clicks to GenArk browsers
  • src/hg/hgc/mafClick.c - lines changed 32, context: html, text, full: html, text

735a45a2ff3e444fe9d668584ad5d221046f0417 Wed May 6 09:02:07 2026 -0700

• correctly reset form after display of existing alignment refs #31811
  • src/hg/js/liftRequest.js - lines changed 13, context: html, text, full: html, text

16bf6ea9e265c3d36d2485cccb9a6ad45a1646d0 Wed May 6 12:05:34 2026 -0700

• additional comments refs #34370
  • src/hg/makeDb/doc/vgp577way/vgp577way.txt - lines changed 25, context: html, text, full: html, text

08402ed691ea91d15ad8fd3daf8b7f8d3578a8d8 Thu May 7 10:53:11 2026 -0700

• VGP 577-way track enabled refs #34370
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/vgp577way.trackDb.ra - lines changed 48, context: html, text, full: html, text

c10a3a45de693f5470abb7ba36b6a1567cbca67c Thu May 7 13:01:04 2026 -0700

• chainNet trackDb for ce11 GCA_000180635.4, otto liftOver
  • src/hg/makeDb/trackDb/worm/ce11/ce11.GCA_000180635.4.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 1, context: html, text, full: html, text

80cbd6bce96d71ce3e03be94934cbff7b4521a4b Thu May 7 13:14:24 2026 -0700

• the trackDb update process for UCSC database assemblies refs #31811
  • src/hg/utils/otto/userRequests/chainNetTrackDb.pl - lines changed 521, context: html, text, full: html, text

2fe7f1d880ccd04daa45aa69719e963981ee3470 Thu May 7 13:36:43 2026 -0700

• updated to work with the galaxy workflow .yaml file refs #31811
  • src/hg/utils/phyloTrees/findScores.pl - lines changed 58, context: html, text, full: html, text

46f246dc334a47ded8a439de133f6d94ef9dae81 Thu May 7 14:40:00 2026 -0700

• now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811
  • src/hg/utils/otto/userRequests/chainNetTrackDb.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 106, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 121, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 44, context: html, text, full: html, text

128037dded4246f2963b7ef08e8f4f1085a6c4eb Thu May 7 14:51:38 2026 -0700

• cron safe full path to hgsql refs #31811
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 4, context: html, text, full: html, text

be8c719942e930d2f4846f231297120d03b4826d Fri May 8 08:15:49 2026 -0700

• fortify against cron job usage full path to hgsql command refs #31811
  • src/hg/makeDb/trackDb/loadTracks - lines changed 3, context: html, text, full: html, text

11f37d009d2ccde22aea894922d55addb6802b07 Fri May 8 09:09:20 2026 -0700

• chainNet trackDb for danRer11 GCA_052040795.1, otto liftOver
  • src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCA_052040795.1.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text

d25bea3289a29e2c24fa84bd84285ecb4a0d1188 Fri May 8 09:14:31 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/loadTracks - lines changed 2, context: html, text, full: html, text

329cf5cc379f5158995d59530a51aafd51dd11cb Fri May 8 09:23:23 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/makefile - lines changed 4, context: html, text, full: html, text

4aa12e0290f91453769f0be4fc5f86ca932fda52 Fri May 8 09:51:50 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/buildRelatedTracks - lines changed 1, context: html, text, full: html, text

a0cc27521dca2ea6d5fe90fb27eef33826dfecba Fri May 8 09:56:48 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/buildTrix - lines changed 4, context: html, text, full: html, text

78377989820616cc99f1e3aca34aca1cd27bafa2 Fri May 8 10:00:45 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/maybeBuildHub - lines changed 6, context: html, text, full: html, text

55ed63b493027583cbd68e954b9ced58d608fba8 Fri May 8 10:15:15 2026 -0700

• fortify against cron job usage full path to kent commands refs #31811
  • src/hg/makeDb/trackDb/checkMetaDb - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hubTxtFromGenArk.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makeMetaDb - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makeTrixLinks - lines changed 1, context: html, text, full: html, text

78be2a814ea9a2f97515f8937b8d1480893b2822 Fri May 8 12:02:51 2026 -0700

• add plasmoDB as a naming scheme
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 1, context: html, text, full: html, text

904f12950eb738c0fba248f3c78a9b0c2d93419c Fri May 8 14:02:21 2026 -0700

• adding an older assembly for P. vivax for BRC refs #34377
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

ad49432690b003435d90afb3f8636a2d4ed5d616 Fri May 8 14:48:58 2026 -0700

• adding a few per user requests
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text

ca8a1a9cc6ae1705396dd14c82ed7e11ccfe9017 Mon May 11 09:20:46 2026 -0700

• chainNet trackDb for danRer11 ce11, otto liftOver
  • src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.ce11.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text

3e52b82695dfd0b5f63b3f5d1505f600647e7143 Mon May 11 09:20:54 2026 -0700

• chainNet trackDb for ce11 danRer11, otto liftOver
  • src/hg/makeDb/trackDb/worm/ce11/ce11.danRer11.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 1, context: html, text, full: html, text