Commits for hiram

v386_preview to v386_preview2 (2019-07-29 to 2019-08-05) v386

d7d97045f093f991875b4bf0efd35d4b928e2967 Mon Jul 29 18:10:16 2019 -0700

• scripts used to build the VGP assembly hubs refs #23734
  • src/hg/makeDb/doc/VGP/amphibian.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/bird.list - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/build.run.list - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/commonNameOrder.list - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/fish.list - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mammal.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkAsmStats.pl - lines changed 264, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkGenomes.pl - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkHubIndex.pl - lines changed 238, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkSymLinks.sh - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/perlPara.pl - lines changed 127, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/runOneJob - lines changed 79, context: html, text, full: html, text

b5e48086053aea919ca5aa06918d0c0f68d66a20 Mon Jul 29 18:59:16 2019 -0700

• adding the .txt files and a README to describe the process refs #23734
  • src/hg/makeDb/doc/VGP/README.txt - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/commonNames.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/genomes.txt - lines changed 231, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/groups.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/hub.txt - lines changed 6, context: html, text, full: html, text

cc0fcb9762d1900766c7e1f1942cbb5561297854 Tue Jul 30 09:55:28 2019 -0700

• allow bigGenePred to open when it is just a bigDataUrl trackDb entry with no associated table refs #23900
  • src/hg/hubApi/apiUtils.c - lines changed 1, context: html, text, full: html, text

d04d32c645edb005fc4811ea1f4e70de6c1c43a5 Tue Jul 30 17:05:54 2019 -0700

• fixup directory name clash for bedJoinTabOffset refs #23806
  • src/userApps/fetchKentSource.sh - lines changed 3, context: html, text, full: html, text

54d189f992b8fd585ade493a3e146f391be03077 Wed Jul 31 11:38:24 2019 -0700

• ampersands in URLs need to be encoded refs #23734
  • src/hg/htdocs/inc/gbFooterHardcoded.html - lines changed 1, context: html, text, full: html, text

8afe6f12967f38da19ce796d17a2510ec47b52ee Wed Jul 31 14:18:47 2019 -0700

• initial original source before jshint improvements refs #23734
  • src/hg/js/sorttable.js - lines changed 495, context: html, text, full: html, text

89cf9d0784b0c1529f4a3638c3255f5b407be611 Wed Jul 31 18:42:44 2019 -0700

• add makefile to function from this source directory and cleaner html output via W3C validator checking refs #23734
  • src/hg/makeDb/doc/VGP/commonNames.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/fish.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/makefile - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mammal.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkAsmStats.pl - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkGenomes.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/mkHubIndex.pl - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/reptile.list - lines changed 1, context: html, text, full: html, text

d84a661a8c877c41a109a21ba4f095d0f26c12c4 Wed Jul 31 18:51:28 2019 -0700

• add assembly report and run during the make refs #23734
  • src/hg/makeDb/doc/VGP/mkSymLinks.sh - lines changed 9, context: html, text, full: html, text

1b17e173bde7713fe7080825f27efb8e952419f4 Thu Aug 1 14:51:39 2019 -0700

• updating text after QA comments refs #23734
  • src/hg/utils/automation/asmHubCpG.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 39, context: html, text, full: html, text

2f9ecbef0ea856db2838ef569c817f7bafd4de09 Thu Aug 1 14:55:29 2019 -0700

• correct word in usage message refs #23918
  • src/hg/utils/automation/gpToIx.pl - lines changed 1, context: html, text, full: html, text

bf57fe2786a732c3e49ae6453aed45b8062b6ed6 Thu Aug 1 14:57:57 2019 -0700

• add twoBitDup check and construct liftOver files and add doNcbiGene refs #23734
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 91, context: html, text, full: html, text

2dc3fec412b817b015deb93f5862e57aea0661b7 Thu Aug 1 16:06:05 2019 -0700

• also update groups.txt if updated here and run up sym links during a make refs #23734
  • src/hg/makeDb/doc/VGP/commonNames.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/VGP/makefile - lines changed 13, context: html, text, full: html, text

100924e5f5169717677039f59ab4fb85099d68d8 Thu Aug 1 16:48:30 2019 -0700

• add VGP outlink refs #23734
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 9, context: html, text, full: html, text

b251152d660f0ccda8732d8312c631ffab31b52e Thu Aug 1 17:14:16 2019 -0700

• cleanup source due to jshint hints, not perfect yet refs #23734
  • src/hg/js/sorttable.js - lines changed 32, context: html, text, full: html, text

3f229b7354bbc99a6fe98e71afd0a0d340c4cc6a Fri Aug 2 09:42:38 2019 -0700

• sorttable is properly an external script refs #23734
  • src/hg/js/external/sorttable.js - lines changed 499, context: html, text, full: html, text
  • src/hg/js/sorttable.js - lines changed 499, context: html, text, full: html, text

c691103685d313c146aded7c45852ac7678267d1 Fri Aug 2 14:31:19 2019 -0700

• do not show itemCounts for containers, they have no items to count refs #23589
  • src/hg/hubApi/list.c - lines changed 6, context: html, text, full: html, text

afeeb82174da7dda62cffcbbf3ffab87194269d6 Fri Aug 2 15:37:49 2019 -0700

• show correct stats for each subTrack in a composite refs #23589
  • src/hg/hubApi/hubApi.c - lines changed 3, context: html, text, full: html, text

7185b2e8f64323c0858f25a5152ea325ee789e3b Fri Aug 2 16:03:22 2019 -0700

• adding sorttable.js to the output refs #23734
  • src/hg/js/external/makefile - lines changed 2, context: html, text, full: html, text

cef25c4a65ad872bda85799c6e2a6d237420c1bc Fri Aug 2 21:46:29 2019 -0700

• now symlink in the photograph for the gateway page refs #23734
  • src/hg/makeDb/doc/VGP/mkSymLinks.sh - lines changed 3, context: html, text, full: html, text

192b2ae780feed3f18c415c42c1de1dbf7bf5be9 Fri Aug 2 21:48:00 2019 -0700

• now with gateway page images refs #23734
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 7, context: html, text, full: html, text

bd5fb0ae8fa613e66280e73e9a6d517f395118db Mon Aug 5 10:36:14 2019 -0700

• v386 preview2, refs #23928
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text