Commits for hiram

v478_preview2 to v478_base (2025-02-17 to 2025-02-24) v478

f57df65b77591fb1aad3208fac9ce2442f658234 Tue Feb 18 15:30:46 2025 -0800

• adding 12 assemblies per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 12, context: html, text, full: html, text

5d7d739e101f89f82ef7c4ce1fdc9a1c413cdef1 Tue Feb 18 19:53:43 2025 -0800

• adding GCA_034509865.1_ASM3450986v1 chicken (Silkie 2023) 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/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text

045f9d50d5be5de9489a7c1e044757aef3469142 Wed Feb 19 09:04:30 2025 -0800

• adding GCA_037788925.1_MytGallo_primary_0.1 Mediterranean mussel (MGYT20220701 primary hap 2024) 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/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

557bc870081c38719069925583655e530ca56920 Wed Feb 19 11:40:10 2025 -0800

• new program tabFmt needs special handling no redmine
  • src/utils/userApps/mkREADME.sh - lines changed 4, context: html, text, full: html, text

5dcb723fb12fbac15ffdd0c3464fce6f722e2e7e Wed Feb 19 13:40:18 2025 -0800

• readjust default visibilities refs #35201
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 6, context: html, text, full: html, text

89f7e9cc7e39854c535c49875835fa1b54bacaa4 Wed Feb 19 13:43:45 2025 -0800

• script to re-run a trackDb build refs #35201
  • src/hg/makeDb/doc/asmHubs/reRunTrackDb.sh - lines changed 54, context: html, text, full: html, text

e82cf3f6e6233075340fa340802429e1f037d7c0 Wed Feb 19 13:53:06 2025 -0800

• using a cut on the file will allow using the order.tsv files refs #35201
  • src/hg/makeDb/doc/asmHubs/reRunTrackDb.sh - lines changed 1, context: html, text, full: html, text

a256e54c8778078498ea06d7447e0d1591090a12 Thu Feb 20 10:03:20 2025 -0800

• added two birds per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text

34e8448fb29e6fd0bf3e6c48e00d53aa8ffdc4ed Thu Feb 20 10:38:04 2025 -0800

• a couple of updates for building on Mac OSX no redmine
  • src/inc/common.mk - lines changed 19, context: html, text, full: html, text

ac0b61420ab00d96616349e7ea289406b9054932 Thu Feb 20 13:01:15 2025 -0800

• tolerant of missing CpG bbi files refs #29545
  • src/hg/utils/automation/asmHubCpG.pl - lines changed 11, context: html, text, full: html, text

87586a71c52ad59bc437786485e7e900cae367ee Mon Feb 24 07:19:52 2025 -0800

• up to date error checking refs #35201
  • src/hg/makeDb/doc/asmHubs/README.txt - lines changed 3, context: html, text, full: html, text

66c18ba2c82bf235f3dcc23936db901d9fb591f9 Mon Feb 24 08:59:39 2025 -0800

• VGP update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 28, 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 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 7, context: html, text, full: html, text