Commits for hiram

v399_preview2 to v399_base (2020-05-25 to 2020-06-01) v399

69809a6ecef72bb253a4191e80c40e426af5d14a Tue May 26 11:15:20 2020 -0700

• fixup rmsk correct composite track definitions and fixup ncbiGene organization refs #23734
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 141, context: html, text, full: html, text

09f1e0f6809ff44752b332ea72c7faacdf085e99 Tue May 26 11:16:06 2020 -0700

• correct usage message refs #23734
  • src/hg/utils/automation/asmHubRmsk.pl - lines changed 1, context: html, text, full: html, text

428bacd2dcbaca9304763d3f2dca7ccffd088caa Tue May 26 11:18:06 2020 -0700

• correct br tags refs #23734
  • src/hg/utils/automation/asmHubNcbiRefSeq.pl - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubXenoRefGene.pl - lines changed 3, context: html, text, full: html, text

3d89934724dbec3c67aa29cd5a1c089e69d611eb Tue May 26 11:19:04 2020 -0700

• remove debug statement refs #23734
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text

5da567339600782c80ebe43ef8b0a2e661b01e94 Wed May 27 11:48:06 2020 -0700

• correct full labels on the groups refs #23734
  • src/hg/makeDb/doc/asmHubs/groups.txt - lines changed 5, context: html, text, full: html, text

f9446c7f0de844971aa819343705a0d6f1ed9eed Wed May 27 12:12:41 2020 -0700

• adding in a few that host Arang.s data tracks refs #23734
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId,asmId.class.txt - lines changed 9, context: html, text, full: html, text

afee0fcf2a7b7de2eb37e1420dc126607373453e Wed May 27 17:31:45 2020 -0700

• rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 16, context: html, text, full: html, text

ded5fbfbae9e713b69de8aeef0efad8719034b07 Wed May 27 17:34:00 2020 -0700

• rework scripts to allow subset hubs to be created from a list of assemblies refs #23734
  • src/hg/makeDb/doc/vgpAsmHub/altMakefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/makefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/trioMakefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/userDataMakefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 72, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 168, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv - lines changed 17, context: html, text, full: html, text

bca05e23f34ba02d4048494770e9ccaa2f178cd5 Thu May 28 12:02:00 2020 -0700

• due to removed duplicates from NCBI assemblies, warn and drop contigs not in the UCSC assembly refs #23734
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text

87580fb0edf5843fed1220d257c8a4edcfcf5a9b Fri May 29 11:19:56 2020 -0700

• starting chainNet per user request refs #25625
  • src/hg/makeDb/doc/mm10.txt - lines changed 69, context: html, text, full: html, text

c8828612e3aba9e6c3072768129de10abe337878 Fri May 29 11:29:04 2020 -0700

• now allow orderList to be specifically stated and begin common set of html functions refs #23734
  • src/hg/makeDb/doc/asmHubs/commonHtml.pm - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 59, context: html, text, full: html, text

c3fdad60d8f01da6ff3296b216015ebae858b06c Fri May 29 17:12:51 2020 -0700

• continue lastz/chain/net run for user refs #25625
  • src/hg/makeDb/doc/mm10.txt - lines changed 26, context: html, text, full: html, text

3eaf4d4b81181d543facc006791bbfc433f26528 Mon Jun 1 09:26:37 2020 -0700

• no need to fail on certificate from genome-source.soe.ucsc.edu refs #25625
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 4, context: html, text, full: html, text