Commits for hiram

d1013ef3c61b027b582a45612ebc3848fe480f3e Mon Apr 7 13:42:08 2025 -0700

now sending to hgdownload3 refs #35402
- src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 10, context: html, text, full: html, text

34ea5c1305694c5e84fc9072ee9a375879895038 Mon Apr 7 13:43:31 2025 -0700

new low track count for BRC project refs #34337
- src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

e9f4a4f731d395f02c435614640e58b0bf919e23 Tue Apr 8 14:29:52 2025 -0700

BRC update and a couple user requests refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/doc/bacteriaAsmHub/bacteria.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
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 8, context: html, text, full: html, text

88a53ecf7f28a5c829fe46eac7297d16fbd8e2e6 Tue Apr 8 18:53:08 2025 -0700

adding one 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 2, context: html, text, full: html, text
- 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

073f999294e187d3ced854717e467a17098972d7 Wed Apr 9 13:21:13 2025 -0700

do not look for genome chrom names/sizes in a database when it is a GenArk hub refs #35479 #34043
- src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text

9862e359bb0b2ee9c1f45331799d059f6a20e702 Wed Apr 9 23:48:38 2025 -0700

VGP update refs #29545
- src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 27, context: html, text, full: html, text
- src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 61, context: html, text, full: html, text
- src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 49, context: html, text, full: html, text

b6ed6ba4a6456f58fa60a91c04aaef0c36728a1d Wed Apr 9 23:52:39 2025 -0700

VGP update refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 12, context: html, text, full: html, text

1785f3fa7c99f5cde3c4ad098681ba1a6675f3eb Wed Apr 9 23:53:46 2025 -0700

common name fixups for VGP update refs #29545
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 6, context: html, text, full: html, text

577743f1021ebf4049429f8257ea3587f01856fd Wed Apr 9 23:54:26 2025 -0700

common name fixups for VGP update refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 10, context: html, text, full: html, text

85933c16175043e83dcf1371fe7a475597e79cf3 Wed Apr 9 23:55:00 2025 -0700

common name fixups for VGP update refs #29545
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

04d3c728227704f2064e5efcc00d358f3e9b7e40 Wed Apr 9 23:55:35 2025 -0700

common name fixups for VGP update refs #29545
- src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 5, context: html, text, full: html, text

4819435d71306cf2fd1d6e48b3c5d488e6eef752 Thu Apr 10 10:46:52 2025 -0700

eliminate duplicate refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text

6addae8d76b1b44013e1e27762268fb8a8d858b5 Thu Apr 10 12:35:47 2025 -0700

correctly make the assemblyList.json for the VGP set refs #34370
- src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 1, context: html, text, full: html, text

a36006a7ddfa0c559bdc43f9437eb476b53e0d52 Thu Apr 10 13:33:50 2025 -0700

8448f5b01d0af06b0b56d5c40f62bac9e5ff202c Fri Apr 11 11:38:08 2025 -0700

2fc83b5b9dc8e08b6f599f99453bde3569b920c2 Fri Apr 11 12:15:15 2025 -0700

VGP update refs #29545
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
- 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

6116bdab443a8dc802081eeb6451dcd889ffa4b5 Sun Apr 13 22:08:28 2025 -0700

1e11c079beed5fcc711c78345614f7367606a94b Sun Apr 13 22:09:36 2025 -0700

VGP update refs #29545
- src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

82c53f775cbff69892c7d009cb27b3c93aba08c2 Mon Apr 14 09:00:37 2025 -0700

VGP update with a new marmoset 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