Commits for hiram

v430_preview to v430_preview2 (2022-04-11 to 2022-04-18) v430

c0f24814891eec0c1c45a0c9d341ae086fa548c7 Mon Apr 11 10:18:25 2022 -0700

• bogus debugging messages removed refs #29203
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 7, context: html, text, full: html, text

7d20b40e8b2cd56b6e37c86f9af31a8d28f24907 Mon Apr 11 11:21:30 2022 -0700

• eliminate obsolete noInherit setting refs #29203
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 1, context: html, text, full: html, text

b1cabf573dc930b78de2f4e5a369c68f7655d9ba Mon Apr 11 15:36:26 2022 -0700

• initial set of files for chm13v2.0 hub construction refs #29203
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.description.html - lines changed 130, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html - lines changed 149, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub.txt - lines changed 618, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.chromAlias.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.faSize.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.groups.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/hub/GCA_009914755.4_T2T-CHM13v2.0_assembly_report.txt - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt - lines changed 591, context: html, text, full: html, text

c5168394dbf70b3d5712c2b613d29e710c5fb23d Mon Apr 11 20:19:57 2022 -0700

• no need for species in gateway page refs #29203
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

70e26b4a27b71aa4844ae0a5aa995e732f8b17e4 Mon Apr 11 21:51:12 2022 -0700

• correct finding queryId report.txt file refs #29203
  • src/hg/utils/automation/asmHubChainNet.pl - lines changed 1, context: html, text, full: html, text

c1085f7ea696f791fc1d258dd6a6f5f3b384a60d Tue Apr 12 09:46:32 2022 -0700

• adding gar.css to the build refs #28930
  • src/hg/htdocs/style/makefile - lines changed 3, context: html, text, full: html, text

d66b075aad8360f3f5130b70cf51c7954ae0a410 Tue Apr 12 13:39:05 2022 -0700

• adding Atlantic salmon per user request refs #29230
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text

5f4eafca0ff4189014f9a214ef0ddbf99ccb6a11 Tue Apr 12 14:14:58 2022 -0700

• now with rsync pushing refs #29203
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 58, context: html, text, full: html, text

8aa1fab06fae584c61a76fa44ef8774856a69000 Tue Apr 12 14:55:41 2022 -0700

• add verifyLogin to prove qateam at hgdownload will work refs #29203
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 5, context: html, text, full: html, text

abb1d7552fcaa56d939b597e72ed53cbb32f8ab9 Tue Apr 12 17:49:49 2022 -0700

• catch up a forgotten runBuild command for GCF_000009045.1_ASM904v1 Bacillus_subtilis no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

e45829e1d7444fd1ffee63a7d0840c81d0e6a619 Tue Apr 12 17:53:05 2022 -0700

• catch up a forgotten runBuild command for GCF_000850965.1_ViralMultiSegProj14847 La_Crosse_virus no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text

8258374ba1d92681de323aee7bd380495044378e Tue Apr 12 18:15:55 2022 -0700

• the assembly GCA_009914755.4_T2T-CHM13v2.0 has been turned into a static set of contents in the source tree no longer automatic here refs #29259
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text

8b151f945031d835c88eb5d2928d0c145c07b058 Tue Apr 12 18:17:10 2022 -0700

• fixup edit errors no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text

46688a248b4634380d5e34ee64b975665a13f53f Tue Apr 12 18:36:24 2022 -0700

• do not need the delete option on the rsync refs #29259
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 1, context: html, text, full: html, text

366e85291a190f6b6a3ac820282132e972375ac8 Wed Apr 13 12:35:45 2022 -0700

• improved text for the chainNet description and adjusting the visibilities of the chainNet tracks refs #29203
  • src/hg/makeDb/doc/chm13v2.0/html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0/trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt - lines changed 43, context: html, text, full: html, text

89ca2e866a3cdf949b93936a84eda90f9d798c80 Wed Apr 13 15:20:52 2022 -0700

• reset track default visibilities refs #29259
  • src/hg/makeDb/doc/chm13v2.0userData/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/censat.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/hgUnique.trackDb.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/rdnaModel.trackDb.txt - lines changed 1, context: html, text, full: html, text

9aea43b079868a83ecf98a717ba26369f0038914 Wed Apr 13 15:21:40 2022 -0700

• reset track default visibilities refs #29259
  • src/hg/makeDb/doc/chm13v2.0/trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt - lines changed 9, context: html, text, full: html, text

458125d8cf4fa7b339c5f3cad7eda29611ad8007 Thu Apr 14 18:11:02 2022 -0700

• this hub.txt does NOT belong in the source tree no redmine
  • src/hg/makeDb/doc/chm13v2.0/hub.txt - lines changed 616, context: html, text, full: html, text

4947432ba44023db07f1dd6be03d39756716aeb1 Thu Apr 14 18:13:09 2022 -0700

• do not leave temporary hub.txt around for garbage no redmine
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 1, context: html, text, full: html, text

b260fe1f52db8c7e5362d4f9db3770409c24e197 Thu Apr 14 18:57:29 2022 -0700

• add the liftOver chainNet tracks refs #29272
  • src/hg/makeDb/trackDb/human/chainNetHuman.ra - lines changed 69, context: html, text, full: html, text

b4d1dfac893a568f669c7f59ab1022047ce50bea Thu Apr 14 20:02:45 2022 -0700

• remove useless list of files and better explain what is happening refs #29203
  • src/hg/makeDb/doc/chm13v2.0/makefile - lines changed 29, context: html, text, full: html, text

ede2fd190d25f754238a2f78b25249d400b596a3 Thu Apr 14 22:10:55 2022 -0700

• fixup the index creation to stuff in the "promoted" hub that is no longer in the tsv listings refs #29259
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 36, context: html, text, full: html, text

cae80adef9ad9f897401c1fbe857eba5bb6679f0 Fri Apr 15 19:06:23 2022 -0700

• always user itemsPerSlot=4 on bedToBigBed for bigMaf.as for performance improvement refs #29263
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 1, context: html, text, full: html, text