Commits for hiram

v461_preview2 to v461_base (2024-02-12 to 2024-02-19) v461

d78f2f29016298f39d54b536b0b51a9ff8ffbff9 Mon Feb 12 15:07:39 2024 -0800

• procedure to add selective annotations to ncbiRefSeq tables refs #32902
  • src/hg/makeDb/doc/mm39/chrM.ncbiRefSeq.txt - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/gffToLink.pl - lines changed 113, context: html, text, full: html, text

fd2b6400802b1b13718080dcef09d10bec1947bd Tue Feb 13 13:01:01 2024 -0800

• adding a couple of assemblies per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

17fcb215cc545daac98634782459e189e6a696a1 Tue Feb 13 13:02:39 2024 -0800

• update a couple of assemblies refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 2, context: html, text, full: html, text

919d6e358931333184e22114fa8fe85e204a8a25 Wed Feb 14 15:08:36 2024 -0800

• also sending out the repeatModeler .stk.gz and .out.gz files no redmine
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 4, context: html, text, full: html, text

5ff5206aee0c9a1b57bc6e8443ec820de0189ad6 Fri Feb 16 09:41:02 2024 -0800

• adding a second Plasmodium to catch up with PlasmoDb refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

e3daa44c78dbe581a4cc1fbdaf071aee36c0e46d Fri Feb 16 10:09:11 2024 -0800

• allow a manual override of chromAuthority refs #29545
  • src/hg/makeDb/doc/asmHubs/chromAuthority.pl - lines changed 10, context: html, text, full: html, text

176447e76f5e9b9a9b37b6e3954587fc4e3cb1c4 Sat Feb 17 22:41:29 2024 -0800

• an update to catch up VGP assemblies refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 9, context: html, text, full: html, text

ac1b89d4efca259844a53e2335769c1fd26b2e79 Mon Feb 19 09:20:31 2024 -0800

• GRCr8 does not exist as a GenArk hub refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text