Commits for hiram

v368_base to v369_preview (2018-07-09 to 2018-07-16) v369

cbb1262183e62300d8b02b003f1ff0b0e602f8ba Mon Jul 9 09:31:59 2018 -0700

• allow maximum sequence count to be defined in hg.conf hgBlat.maxSequenceCount no redmine
  • src/hg/hgBlat/hgBlat.c - lines changed 6, context: html, text, full: html, text

bd81937d0a0aa0198bb47969902260ba29731e5d Tue Jul 10 10:29:57 2018 -0700

• adding ambMex1 Axolotl refs #21715
  • src/hg/utils/phyloTrees/220.nh - lines changed 220, context: html, text, full: html, text

511e00386c784f37a43aca45a5367c068a2dccc4 Tue Jul 10 11:03:23 2018 -0700

• adding ambMex1 Axolotl - Ambystoma mexicanum
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

b7a925d39b4755947047aaf047c94c957a13cb36 Tue Jul 10 11:32:51 2018 -0700

• adding gold table assembly track search rule refs #21715
  • src/hg/makeDb/trackDb/axolotl/ambMex1/trackDb.ra - lines changed 5, context: html, text, full: html, text

74425b74c2d4cd28a8ef90a5748e9c6f92b25a62 Tue Jul 10 11:34:08 2018 -0700

• added genbank definitions running up mm10 lastz chainNet refs #21715
  • src/hg/makeDb/doc/ambMex1/initialBuild.txt - lines changed 439, context: html, text, full: html, text

62ea85fa943b018907c42aff118199b80fee20f5 Tue Jul 10 11:35:07 2018 -0700

• script to manage to this gigantic genome refs #21715
  • src/hg/makeDb/doc/ambMex1/twoGbChunks.pl - lines changed 68, context: html, text, full: html, text

cb473e9cc9f1013ca21d300b852873864f87e2aa Tue Jul 10 11:40:24 2018 -0700

• add allowBridged option refs #21715
  • src/hg/utils/gapToLift/gapToLift.c - lines changed 6, context: html, text, full: html, text

68edf4def88d67a6728778c61172135af46edfe6 Tue Jul 10 11:42:50 2018 -0700

• adding ambMex1/axolotl refs #21715
  • 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 1, context: html, text, full: html, text

d069f32c28cd22141e4ba10e9eedd63db9c0e13c Tue Jul 10 11:44:20 2018 -0700

• turning on signal for genbank to run refs #21715
  • src/hg/makeDb/doc/ambMex1/initialBuild.txt - lines changed 8, context: html, text, full: html, text

89f62bfd8aee9fabba868d186fe9bb38acafd678 Tue Jul 10 13:17:11 2018 -0700

• lastz chain net run to ambMex1 refs #21715
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 80, context: html, text, full: html, text

8265e44093ad21c6366b8260b8f5a7f6ed7ad50a Tue Jul 10 13:48:39 2018 -0700

• adding definitions for chainNet to Axolotl refs #21715
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra - lines changed 58, context: html, text, full: html, text

075e7086a8c68293fc7cb05cc2fd64f7108f47cd Wed Jul 11 09:37:49 2018 -0700

• lastz chain net to ambMex1 refs #21715
  • src/hg/makeDb/doc/mm10.txt - lines changed 83, context: html, text, full: html, text

b812219ab79f0f6ae871974803764dc6f885cd7a Wed Jul 11 09:41:06 2018 -0700

• lastz chain net swaps from hg38 and mm10 refs #21715
  • src/hg/makeDb/doc/ambMex1/initialBuild.txt - lines changed 35, context: html, text, full: html, text

dfe26d626345b785d82a952ae9e61984e9949222 Wed Jul 11 09:49:47 2018 -0700

• adding ambMex1 rules refs #21715
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text

56a3dccf5300faad732bb3a9f653112714e77a47 Wed Jul 11 10:22:40 2018 -0700

• updated to manage mnt and export from hub as mnt/data refs #18874
  • src/hg/utils/automation/openStack/paraNodeSetup.sh.template - lines changed 24, context: html, text, full: html, text

99bd950f66d2ab880841a0867d1ef883ac5c04fa Wed Jul 11 14:23:14 2018 -0700

• NFS exports needs to happen earlier refs #18874
  • src/hg/utils/automation/openStack/paraHubSetup.sh - lines changed 42, context: html, text, full: html, text

5217655c0cbb3b72529f5d92ea4e37d1cf8a7618 Thu Jul 12 09:33:47 2018 -0700

• correctly setup /mnt/data/ refs #18874
  • src/hg/utils/automation/openStack/paraHubSetup.sh - lines changed 4, context: html, text, full: html, text

881b58fb84858be273ecc0a0437f48531b8ac213 Thu Jul 12 11:23:37 2018 -0700

• correctly remove and add machines when resurrecting nodes refs #18874
  • src/hg/utils/automation/openStack/initParasol - lines changed 6, context: html, text, full: html, text

15bbec7f5dca3361b54d138109f240dc178b8eb5 Thu Jul 12 16:21:13 2018 -0700

• default viz on tracks to make an interesting display at default position on PAX7 gene refs #21715
  • src/hg/makeDb/trackDb/axolotl/ambMex1/trackDb.ra - lines changed 34, context: html, text, full: html, text

f71f3e5656f50a221cfe8dba528480db1c34c35e Thu Jul 12 17:14:53 2018 -0700

• override cpgIslanSuper visibilities refs #21715
  • src/hg/makeDb/trackDb/axolotl/ambMex1/trackDb.ra - lines changed 7, context: html, text, full: html, text

b199702ea2e5425fe84d4d1f47ee9ba26424a361 Thu Jul 12 17:17:23 2018 -0700

• visibility on a super track is meaningless refs #21715
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text

9332df756fb318c4bd7c3fc4a031b718f8b668ba Fri Jul 13 09:32:40 2018 -0700

• QA Ready with no blat server refs #21715
  • src/hg/makeDb/doc/ambMex1/initialBuild.txt - lines changed 29, context: html, text, full: html, text

6560d2ee6dec726908f1e230e7d75cec06d4c58a Mon Jul 16 10:06:33 2018 -0700

• v369 preview1, refs #21667
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text