Commits for hiram

v406_preview to v406_preview2 (2020-10-12 to 2020-10-19) v406

093ec075d6dd84496e38c5f5f110bf4b4c54298b Tue Oct 13 11:14:51 2020 -0700

• begin bacteria hub with an E. coli requested by user refs #26347
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/hub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/makefile - lines changed 26, context: html, text, full: html, text

4da1a14630708d887c3481e3b16df5044c86c59a Tue Oct 13 11:16:59 2020 -0700

• better batch size for xenoRefGene and fixup to handle assemblies without repeat masker and RM can not run on those species refs #26347
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 36, context: html, text, full: html, text
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 5, context: html, text, full: html, text

2390b850402fec79626ff5958af79779352c9d84 Thu Oct 15 08:54:38 2020 -0700

• clean up obsolete files refs #24748
  • src/hg/makeDb/doc/asmHubs/mammals.asmId.commonName.tsv - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mammals.commonName.asmId.orderList.tsv - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/primates.asmId.commonName.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/primates.commonName.asmId.orderList.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/vertebrate.asmId.commonName.tsv - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/vertebrate.commonName.asmId.orderList.tsv - lines changed 25, context: html, text, full: html, text

393d6e8e6a2d75158342a665d71093b3569ae0ee Thu Oct 15 08:57:51 2020 -0700

• rsync with delete is OK refs #23891
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 1, context: html, text, full: html, text

eb5f674d8ebadc542e4fbad84e465a629bdee6c7 Thu Oct 15 09:17:33 2020 -0700

• correctly create near mis list refs #24547
  • src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh - lines changed 1, context: html, text, full: html, text

272a25f286c4041d89fa5c159a1c2b59d6d78271 Thu Oct 15 09:19:39 2020 -0700

• add gene name to pop message for LRG track refs #24672
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 14, context: html, text, full: html, text

9767ea420ca35a45c6ed2c81f7bc7fde1ca30373 Thu Oct 15 09:22:16 2020 -0700

• adding more bigZips files for genes gtf files, and clarify wild card expansion ro redmine
  • src/hg/utils/automation/makePushQSql.pl - lines changed 1, context: html, text, full: html, text

90b9985e1fc9106341b275badcd445531be9a48c Thu Oct 15 09:23:22 2020 -0700

• add noAugustus and noXenoRefSeq options for bacteria hub build refs #23891
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 23, context: html, text, full: html, text

1857a999455044505e7c0395b5b6b68b59c15906 Thu Oct 15 09:25:58 2020 -0700

• allow optional user data tracks in a trackDb (VGP work) refs #23891
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 5, context: html, text, full: html, text

b707eeb51bad2091d226fc58e025fde1c7646c94 Fri Oct 16 16:09:40 2020 -0700

• initial prototype of wiggle mouse over values, it is really slow refs #21980
  • src/hg/hgTracks/wigTrack.c - lines changed 96, context: html, text, full: html, text

211722d8a12ca7202c4401453a93d7d606aa7d4f Mon Oct 19 08:45:04 2020 -0700

• turn off the wiggle mouse overs until better solution found refs #21980
  • src/hg/hgTracks/wigTrack.c - lines changed 2, context: html, text, full: html, text