Commits for hiram

v410_preview2 to v410_base (2021-02-01 to 2021-02-08) v410

9cb1c014fe8ede37d3bf519a62746731b44c7bc5 Tue Feb 2 07:06:05 2021 -0800

• style update code review refs #26904
  • src/hg/js/hgTracks.js - lines changed 3, context: html, text, full: html, text

ac0ae4405481be61afc8f6e74d67aeac6b6f0e64 Tue Feb 2 11:07:48 2021 -0800

• fix SQL query missing closing paren refs #26893 #24074
  • src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text

6b96e53a208eaadaf940e392a5decc7f83a1e859 Tue Feb 2 13:25:01 2021 -0800

• catching up recently finished assembly hub builds and uniq common names refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 14, context: html, text, full: html, text

13ca91a9d4a1ed3169fb78c4f39be9cbe5eb4869 Tue Feb 2 14:48:17 2021 -0800

• scripts used on hgdownload to construct text list of hubs and top level index.html page refs #23891
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 210, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/hubList.sh - lines changed 46, context: html, text, full: html, text

e204336831dd2fccd93b1aabc4d647c933ba8dbc Tue Feb 2 14:53:39 2021 -0800

• fixup a couple names refs #23891
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - 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/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text

1c60aec14fd14f3594fbbfe765f3594223e36f25 Tue Feb 2 14:54:28 2021 -0800

• adding the troublesome primate assembly refs #23891
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

6f3824a64a095636d23b144a7536a1f5a8779f07 Tue Feb 2 14:54:54 2021 -0800

• better error exit on broken orderList refs #23891
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 4, context: html, text, full: html, text

fc0e57ce770bea86faa7e4f6b4c83197d335257b Wed Feb 3 16:25:45 2021 -0800

• initial files for rn7 refs #26682
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn7/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn7/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn7/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn7/trackDb.ra - lines changed 8, context: html, text, full: html, text

9cc7ce1af6119158545ad718793c5066ee69249c Wed Feb 3 16:35:45 2021 -0800

• adding search rule for gold/assembly track refs #26682
  • src/hg/makeDb/trackDb/rat/rn7/trackDb.ra - lines changed 6, context: html, text, full: html, text

102685aae3c6965281c5de9b14337f73995c204f Wed Feb 3 16:59:19 2021 -0800

• running repeat masker and simple repeats refs #26682
  • src/hg/makeDb/doc/rn7/initialBuild.txt - lines changed 1256, context: html, text, full: html, text

e8d55d40ff0495dd97941c256f810b6505955e7e Wed Feb 3 21:53:39 2021 -0800

• the Plants hub is obsolete for a default now using Synonymous Constraint no redmine
  • src/hg/hubApi/hubApi.c - lines changed 1, context: html, text, full: html, text

e26e5b3e3ef27f2cdab7877d465e50b73f25508c Thu Feb 4 09:42:23 2021 -0800

• Added rn7 rat refs #26682
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 18, context: html, text, full: html, text

8227afe8706dad285f0bcef3213f8e4643f899d4 Thu Feb 4 09:44:06 2021 -0800

• Added rn7 - rat refs #26682
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 4, context: html, text, full: html, text

e9ce87fb66d90958cbbdfdbec1a1a3c4556f0239 Thu Feb 4 09:58:23 2021 -0800

• NCBI ClonDB url is obsolete refs #21948
  • src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/cloneEnd.trackDb.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/cloneEnd.trackDb.ra - lines changed 12, context: html, text, full: html, text

476457cc05d68579e4502302dd731225d068b7d2 Thu Feb 4 10:37:16 2021 -0800

• addin NCBI RefSeq composite track refs #26682
  • src/hg/makeDb/trackDb/rat/rn7/trackDb.ra - lines changed 1, context: html, text, full: html, text

78173ba6a8a9e90fda4863cdf2712708ca7d7ea3 Thu Feb 4 10:53:09 2021 -0800

• adding rules for rn7 refs #26682
  • src/hg/makeDb/schema/all.joiner - lines changed 7, context: html, text, full: html, text

d42b1cf12daaba8db0c8faa736548d6d1edb0f30 Fri Feb 5 13:21:16 2021 -0800

• adding make doc for the runs that were all automatic refs #26815
  • src/hg/makeDb/doc/mm39/lastzRuns.txt - lines changed 1592, context: html, text, full: html, text

7c10410f740fc07c6ee0a49cdad69fca9b3cdbaf Fri Feb 5 15:21:49 2021 -0800

• beginning to add chainNet tracks to assembly hubs refs #26815
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 178, context: html, text, full: html, text