Commits for hiram

5c59ddc77713387809ce52e0e553eeb3e7b7ee64 Mon May 19 12:57:47 2025 -0700

better explicit recognition of hs1 oddities refs #35712
- src/hg/utils/automation/doRecipBest.pl - lines changed 14, context: html, text, full: html, text

6619816b39594b4cafca3215c7d8ac4dfd185652 Tue May 20 14:50:43 2025 -0700

document procedure for Tiberius gene predictions addition to GenArk hubs refs #34917
- src/hg/makeDb/doc/tiberius.txt - lines changed 220, context: html, text, full: html, text

74e53377949096d1ea6f3d78ec59b1914f1373d8 Tue May 20 14:58:35 2025 -0700

note about trackDb files and beta and public release control refs #34917
- src/hg/makeDb/doc/tiberius.txt - lines changed 24, context: html, text, full: html, text

02f4db8b8cb4a5fce01f05c91f2dd48bb4e4b1ac Tue May 20 15:05:30 2025 -0700

indicate how the alpha version can be seen on genome-test refs #34917
- src/hg/makeDb/doc/tiberius.txt - lines changed 12, context: html, text, full: html, text

083fc14e534ca67e2355bab5b3e8f399bb0dc1f4 Wed May 21 12:22:52 2025 -0700

beware some viral genomes will not have ix ixx files for ncbiGene track refs #34337
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 2, context: html, text, full: html, text
- src/hg/utils/automation/doAssemblyHub.pl - lines changed 2, context: html, text, full: html, text

c7bad6715f205dc408321934c1a81826fb62c6f3 Wed May 21 12:26:14 2025 -0700

adding one per user request refs #29545
- src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

76cfe27c9284feea7aa0c597b68ae7235fe24205 Wed May 21 12:54:05 2025 -0700

adding one for the BRC project refs #34337
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

07a637e0db9080685f99bc24e161858cb3094b41 Thu May 22 13:55:53 2025 -0700

correct URL outlink on name2 field for NCBI RefSeq gene tracks refs #34704
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 3, context: html, text, full: html, text

0800aafe419bb4a252a0656a75b83e89ef27ec20 Thu May 22 14:20:58 2025 -0700

use standard UCSC format for reference refs #34917
- src/hg/makeDb/trackDb/contrib/tiberius/Tiberius.html - lines changed 13, context: html, text, full: html, text

4188ce8621f2ed8565863a04cf1743cad5a971a8 Thu May 22 15:25:52 2025 -0700

turn off score filter for the trackUi page since all scores are zero refs #34917
- src/hg/makeDb/trackDb/contrib/tiberius/tiberius.trackDb.txt - lines changed 1, context: html, text, full: html, text

1015a6b47a62f5dd44c8b57730103237c6808366 Sat May 24 07:32:19 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/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

a391c724e8ae7c5b72ef6248a7ce6a8c57f7a8ed Sun May 25 23:00:29 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/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text

958df42e01d6a9392368bd24fe483b152c0c5ac7 Mon May 26 13:37:11 2025 -0700

adding two 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/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 2, context: html, text, full: html, text