Commits for hiram

v472_preview to v472_preview2 (2024-09-23 to 2024-09-30) v472

36a317dc1cd15748c1fe2b18eef4991141fe1464 Mon Sep 23 15:13:11 2024 -0700

• BRC update moved some to legacy refs #34337
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 6, context: html, text, full: html, text

c4c8fc39c7091c0f19878c93f8b92897c756b95d Mon Sep 23 15:15:11 2024 -0700

• BRC moved one to legacy refs #34337
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

772a45f22132de29b8ab26d4b42a2c0fe6088ae5 Tue Sep 24 10:16:18 2024 -0700

• BRC update nearing completion refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 15, context: html, text, full: html, text

f9f8a289464407f2f6a3337760bf8270d2117517 Tue Sep 24 14:36:40 2024 -0700

• asmHubs/master.run.list
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text

47ed7b59bcc5fb7777382709b4ae4e3b27ba2b5a Tue Sep 24 14:37:08 2024 -0700

• eliminate some duplicates refs $34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text

9cf3f9dfbd2770a517953c7f43ffade95be9a9de Tue Sep 24 15:26:53 2024 -0700

• add the ucscBrowser link to the stderr outpur ref #34337
  • src/hg/makeDb/doc/asmHubs/tsvToJson.py - lines changed 2, context: html, text, full: html, text

444891eef90db1bdbff678ed49c19f3fd5c9f68d Tue Sep 24 15:31:27 2024 -0700

• do not try to send UCSC database browsers refs #34337
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 4, context: html, text, full: html, text

9d9f00e7ae0c4007130239f651fbc587f25f244f Tue Sep 24 23:02:55 2024 -0700

• eliminate specific references to hgcentraltest refs #32596
  • src/hg/hubApi/findGenome.c - lines changed 20, context: html, text, full: html, text

9a4f1d0a4e48296598ef888c93c89930518ed59b Wed Sep 25 14:36:20 2024 -0700

• eliminate some duplicates refs #34337
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 6, 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 5, context: html, text, full: html, text

766cc89bdfe27cfd40cd68e46eb266dccdfe6077 Wed Sep 25 23:28:03 2024 -0700

• BRC update refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 9, context: html, text, full: html, text

6cb05644f9dc2dcb89eba11052f5a218116c083c Thu Sep 26 08:52:03 2024 -0700

• eliminate mistaken duplicates refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

22125620d4dc7d776599c3bf6e99932ba43a6db5 Thu Sep 26 10:28:21 2024 -0700

• allow an assembly to work even if it has no repeatMasker result refs #34337
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 6, context: html, text, full: html, text

ea5d663f1b5af778bb8ba4d10d956d248c9566c2 Thu Sep 26 14:28:03 2024 -0700

• BRC update gets up to 769 refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 9, context: html, text, full: html, text

2776159fd4f68c3c5a1a114f238dc2f568a5bd64 Fri Sep 27 11:07:16 2024 -0700

• allow use of new genark table with more columns refs #32596
  • src/hg/hgGateway/hgGateway.c - lines changed 11, context: html, text, full: html, text

e7b66711387ac5b785cd52148ca4ce1180609167 Fri Sep 27 11:13:00 2024 -0700

• add the FULLTEXT index refs #32596
  • src/hg/lib/genark.sql - lines changed 1, context: html, text, full: html, text

736e0d588f220cef8093cf1ba6ea3bb4f376baf4 Fri Sep 27 11:25:40 2024 -0700

• now loading up the new expanded genark.hgcentral table refs #32596
  • src/hg/utils/otto/genArk/README - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/addAssemblyList.sh - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/dbDb.clade.year.acc.tsv - lines changed 248, context: html, text, full: html, text

621822a450d38d641f59df03aa461fa7dba64da6 Fri Sep 27 15:24:08 2024 -0700

• now with one word searches on the assemblyList table refs #32596
  • src/hg/hgGateway/hgGateway.c - lines changed 71, context: html, text, full: html, text

5442a9baf9e3667418b1dbda2225d9c9389b7249 Fri Sep 27 15:35:26 2024 -0700

• order by priority for the assemblyList result refs #32596
  • src/hg/hgGateway/hgGateway.c - lines changed 2, context: html, text, full: html, text

e5297f22c5d7c1cb0b041b0ea4c66206a244c90b Mon Sep 30 10:36:52 2024 -0700

• add multiple word search to the hgGateway assembly search box function refs #32596
  • src/hg/hgGateway/hgGateway.c - lines changed 8, context: html, text, full: html, text
  • src/hg/inc/assemblyList.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/assemblyList.c - lines changed 40, context: html, text, full: html, text

ccda596950ffdad4d7560c1bb660b31c1bd3b55a Mon Sep 30 11:07:54 2024 -0700

• put a limit on genark returned list refs #32596
  • src/hg/hgGateway/hgGateway.c - lines changed 8, context: html, text, full: html, text