Commits for hiram

v424_preview2 to v424_base (2021-11-22 to 2021-12-06) v424

8dddffded74dff5108fa03a4e64d7e9f4040cd47 Tue Nov 23 07:24:49 2021 -0800

• fixup bcsh->bash script name refs #28457
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 1, context: html, text, full: html, text

1e87a5e306cb4602fb6781077be0265db2d58c4f Wed Dec 1 11:29:46 2021 -0800

• update scripts for new location refs #28331
  • src/hg/utils/otto/grcIncident/README.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/grcUpdate.sh - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/runUpdate.sh - lines changed 43, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/verifyTransfer.sh - lines changed 47, context: html, text, full: html, text

371a636b6cf6c5c48f41be953541a62eea58db84 Wed Dec 1 11:31:37 2021 -0800

• grcIncident seems to be working OK refs #28331
  • src/hg/utils/otto/otto.crontab - lines changed 2, context: html, text, full: html, text

2ec1b855bf15da994b011482b39f7a4306dc84a1 Wed Dec 1 12:12:56 2021 -0800

• update to run from /hive/data/outside/otto/ncbiRefSeq/ refs #28331
  • src/hg/utils/otto/ncbiRefSeq/README.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/ottoNcbiRefSeq.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runHg19.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runHg38.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runMm10.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runMm39.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh - lines changed 1, context: html, text, full: html, text

e73767fd1017611f858e067f55f3557a99f983f4 Wed Dec 1 12:28:40 2021 -0800

• adding Lou email for the notices refs #28331
  • src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh - lines changed 2, context: html, text, full: html, text

d20db35e0061e340168b2457d66dbae67db49437 Wed Dec 1 12:32:01 2021 -0800

• hg38 updated during testing refs #28331
  • src/hg/utils/otto/ncbiRefSeq/prevHg38.sum - lines changed 1, context: html, text, full: html, text

ccb2746595a0661a942db277329de7d3fbfdd80a Wed Dec 1 12:34:15 2021 -0800

• turning on ncbiRefSeq job refs #28331
  • src/hg/utils/otto/otto.crontab - lines changed 2, context: html, text, full: html, text

a8a20738a644d24872835b8ef5e0d9608bdd3bdf Wed Dec 1 15:40:57 2021 -0800

• do not fail on empty genePred for ncbiGene no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

0c48fdb70c330626acba56d84e4c4a48b8964693 Thu Dec 2 11:40:57 2021 -0800

• large performance improvement, better splitting procedure and smaller cluster batch sizes for high contig count assemblies no redmine
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 16, context: html, text, full: html, text

4f32f0ed3a5bf91211465c8db671ab88148b241d Fri Dec 3 14:15:36 2021 -0800

• add a separate target for just the index pages no redmine
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 14, context: html, text, full: html, text

4c3db3474f70fda782defb5d547412877413d5a7 Fri Dec 3 14:16:30 2021 -0800

• use the ROOT var to establish the path to sorttable.js no redmine
  • src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 1, context: html, text, full: html, text

1d146045a364ba90cc1d5e04e376e0d3a87441ac Fri Dec 3 14:16:45 2021 -0800

• use the ROOT var to establish the path to sorttable.js no redmine
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 3, context: html, text, full: html, text

d9c1bc641f6274ed752c0565b4b5b0276efb3340 Fri Dec 3 14:19:00 2021 -0800

• adding the sequence NP_389226.1.prot for other organisms outside vertebrates no redmine
  • src/hg/makeDb/doc/asmHubs/rtp1.ace2.faa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

ab0447a17c1443afa4d0a66f38621cfeb9afbae7 Fri Dec 3 14:23:26 2021 -0800

• adding bread wheat GCA_907166925.1_wheat_cv_fielder_v1_assembly per user request
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text

c8bcd3174e6625afbd8e6b0039f1077afb2b6391 Fri Dec 3 14:24:31 2021 -0800

• fixup incorrect shortLabel on RBest Chain no redmine
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 1, context: html, text, full: html, text

016dc9eaa7c179b628f450b6d3a2eed84805b752 Fri Dec 3 14:25:42 2021 -0800

• starting zoo241 hub listings no redmine
  • src/hg/makeDb/doc/zoonomiaAsmHub/makefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/zoonomiaAsmHub/zoonomia.orderList.tsv - lines changed 241, context: html, text, full: html, text

89612d81c4d63c4dde4e0cc7601cb927e5d8d5ff Sun Dec 5 16:19:30 2021 -0800

• adding new Ferret assembly per D. Haussler request GCF_011764305.1_ASM1176430v1.1 no redmine
  • 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/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text