Commits for hiram

v445_base to v446_preview (2023-03-13 to 2023-03-20) v446

540d6e9c29612d2a2a932e04bc917ab73a442401 Mon Mar 13 11:00:47 2023 -0700

• adding GCF_027579735.1_aBomBom1.pri fire-bellied toad (aBomBom1 primary hap 2023) per user for RefSeq update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

37421ec79ef8877da0fd40cb21335fa61e36475a Mon Mar 13 11:33:59 2023 -0700

• starting two example HPRC assemblies refs #30508
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text

6d95fbd4185c76a8bedb7e5115bd0b5bd34ac0e0 Mon Mar 13 13:43:28 2023 -0700

• adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) 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/legacyAsmHub/legacy.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

674e99d2258f5a334cb0badb20a1e437debe7ca1 Mon Mar 13 13:45:05 2023 -0700

• adding GCA_904849725.1_MorexV3_pseudomolecules_assembly domesticated barley (H.vulgare 2021 genbank) per user request refs #29545
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 11, context: html, text, full: html, text

2e5bad70bb2d00c524f3b3ee630b67c1b67b7d89 Mon Mar 13 15:22:27 2023 -0700

• adding 4 more for RefSeq update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 6, context: html, text, full: html, text

923105258f47bd9b394d707c53e8626856403bfb Mon Mar 13 16:39:26 2023 -0700

• adding four to catch up RefSeq assemblies refs #29545
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 2, context: html, text, full: html, text

46d1b1ddb8160c5203eca5ae39302374eea74c64 Wed Mar 15 10:43:28 2023 -0700

• enforce using HAL *only* on hgwdev, no other machine, breaks userApps build on hgcompute-01 no redmine
  • src/inc/common.mk - lines changed 3, context: html, text, full: html, text

7fb4fbe8a776a07fd04922670e4ffac45e7dae60 Wed Mar 15 14:28:41 2023 -0700

• adding 5 more HPRC builds ref #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 5, context: html, text, full: html, text

8d8aeeae86fd9c8d88d199fb03b4fe8c2e381c1d Wed Mar 15 14:45:34 2023 -0700

• adding 5 more HPRC builds ref #29545
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 5, context: html, text, full: html, text

23afc99533e828beee0252880a28eee1bd885870 Wed Mar 15 20:31:40 2023 -0700

• starting HPRC with 9 genomes refs #30508
  • src/hg/makeDb/doc/hprcAsmHub/hprc.orderList.tsv - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/hprcAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hprcAsmHub/makefile - lines changed 23, context: html, text, full: html, text

ff3005ab6eb18c0111dc8a08c5a5ff057c79a1d5 Wed Mar 15 20:44:33 2023 -0700

• HPRC logo from https://humanpangenome.org/img/Logo-3.png refs #30508
  • src/hg/makeDb/doc/hprcAsmHub/HPRC_PanGenome_Logo.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 Wed Mar 15 21:16:40 2023 -0700

• adding HPRC links to the index pages refs #30508
  • src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 23, context: html, text, full: html, text

c44435c2093a2967aa189ef7394595edcc7cbf3d Wed Mar 15 21:25:07 2023 -0700

• adding viral and bacteria index pointers no redmine
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 14, context: html, text, full: html, text

653a69b696a8534261a8ff0dcbf1ef3af7d7c816 Wed Mar 15 21:45:32 2023 -0700

• adding link to HPRC collection no redmine
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 13, context: html, text, full: html, text

620c0f6f7951ebe04d3599ed66ac6a46e36edbaf Wed Mar 15 21:48:36 2023 -0700

• extra table header can center its text no redmine
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 1, context: html, text, full: html, text

bc7b8c2d05214b6e6ebe5d7b99d8361394d3c3d5 Wed Mar 15 21:50:12 2023 -0700

• do not want sortable table since it now has an extra header in the middle no redmine
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 2, context: html, text, full: html, text

d2d394ba518c610ec0a1a23a114b2f7bb518828c Thu Mar 16 11:15:19 2023 -0700

• catching up the 20 HPRC assemblies refs #30508
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 14, context: html, text, full: html, text

f436af2460ce80a02f8e6c12dc9482c1a0957172 Thu Mar 16 12:01:34 2023 -0700

• catching up 20 HPRC genomes refs #30508
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 14, context: html, text, full: html, text

da5c2bf40e5fa78b2e072c52069d6bbf71a6f469 Thu Mar 16 14:32:36 2023 -0700

• script to make the alias table tsv after the assemblyRequest page has been made refs #30474
  • src/hg/gar/mkAlias.pl - lines changed 205, context: html, text, full: html, text

cd9835e35a7381da350289f1eb287005bfac1826 Fri Mar 17 13:22:45 2023 -0700

• fixup makefile to show server and allow other targets for convenient server setting refs #30457
  • src/hg/hubApi/tests/expected/err48.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/err49.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/makefile - lines changed 168, context: html, text, full: html, text

4c458a517cc3ea3cfa4f26a2c136d3641647edd2 Fri Mar 17 15:03:41 2023 -0700

• adding a search test refs #24113
  • src/hg/hubApi/tests/makefile - lines changed 25, context: html, text, full: html, text

3227ff50033faf22cb1199ad40610f9042c7fd10 Fri Mar 17 16:19:21 2023 -0700

• add special section for the VGP index page to point to the special listings of files no redmine
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 18, context: html, text, full: html, text

90006ce50a15349235c0defdc272526fe1b48aa1 Sat Mar 18 09:13:46 2023 -0700

• adding three per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text

4516d025b57857bdddbf393f5d82c6c2b91e22c3 Sat Mar 18 09:26:01 2023 -0700

• adding three per user request refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 3, context: html, text, full: html, text