Commits for hiram

v347_preview2 to v347_base (2017-03-27 to 2017-04-03) v347

558172af273129615a2adbae6c8d8862404b3d4d Mon Mar 27 13:26:12 2017 -0700

• starting xenTro9 browser build refs #19151
  • src/hg/makeDb/doc/xenTro9/initialBuild.txt - lines changed 820, context: html, text, full: html, text

2fafa17e1e857dbf37a65ec4ccd721b6c3d7d7d5 Mon Mar 27 13:48:24 2017 -0700

• need to have trackDb.chainNet.other.ra present refs #19151
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text

a3880d7ba279b70cbbc51129e3fb92552e0133d8 Mon Mar 27 13:52:11 2017 -0700

• adding xenTro9 to the build refs #19151
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra - lines changed 8, context: html, text, full: html, text

2ff2df7e6108aa43be643a90608349fc04607200 Mon Mar 27 14:49:57 2017 -0700

• add search rule for gold table refs #15515
  • src/hg/makeDb/trackDb/pangolin/manPen1/trackDb.ra - lines changed 5, context: html, text, full: html, text

93b3630bbcacbdefacda25f40c6a785f54b5a766 Mon Mar 27 14:51:38 2017 -0700

• adding gold table search rule refs #15515
  • src/hg/makeDb/doc/manPen1/initialBuild.txt - lines changed 19, context: html, text, full: html, text

22341ea540b0cfb603995bc2897e9e0655848977 Mon Mar 27 14:54:55 2017 -0700

• adding gold table search rule refs #19151
  • src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.ra - lines changed 5, context: html, text, full: html, text

e924cc0c4b68332ef6258eca1fa72c3c53b32a0b Tue Mar 28 09:57:23 2017 -0700

• fixup biosample reference refs #19151
  • src/hg/makeDb/trackDb/drosophila/droSim2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macNem1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/description.html - lines changed 1, context: html, text, full: html, text

8b48f7cfea69513a415605c9672c0d43982df8b3 Tue Mar 28 10:00:22 2017 -0700

• fixup biosample reference refs #19151
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text

25c631fc8b79b34d3db19c482a979c16360c21f7 Tue Mar 28 10:18:44 2017 -0700

• adding xenTro9 X, tropicalis refs #19151
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 21, context: html, text, full: html, text

f0e2998a468ec328f3336cde01a4e1b9e3273e59 Tue Mar 28 10:25:20 2017 -0700

• working up a small 4-way for Juergen refs #10146
  • src/hg/makeDb/doc/tupChi1/multiz4way.txt - lines changed 1461, context: html, text, full: html, text

9e09a1d7d6dd7c108c30c580ba5a9631a37fb0c8 Tue Mar 28 11:59:12 2017 -0700

• adding 4-way alignment refs #10146
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html - lines changed 427, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.4way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra - lines changed 2, context: html, text, full: html, text

45ea203bc940e6218145977baa26078b8f6e11ca Tue Mar 28 12:06:03 2017 -0700

• 4-way downloads done refs #10146
  • src/hg/makeDb/doc/tupChi1/multiz4way.txt - lines changed 39, context: html, text, full: html, text

347ccb4b97cc6262b17f951a97f0eb49f81d8a04 Tue Mar 28 13:49:21 2017 -0700

• may as well use the string that has been carefully constructed refs #19079
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text

27fda4ff70c44812f24c5b3f70a6b712996d3882 Wed Mar 29 10:04:24 2017 -0700

• adding xenTro9 to the update alignments refs #19151
  • 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 2, context: html, text, full: html, text

7b3800545b5c348f619b01a73847cf219f71da48 Wed Mar 29 10:19:09 2017 -0700

• adding xenTro9 rules refs #19151
  • src/hg/makeDb/schema/all.joiner - lines changed 11, context: html, text, full: html, text

3aa8f8f910395a46660ba59d42987df23fc6a453 Wed Mar 29 14:18:10 2017 -0700

• recording the schema for ncbiRefSeqOther extended bigBed schema refs #13673
  • src/hg/inc/ncbiRefSeqOther.as - lines changed 36, context: html, text, full: html, text

18ff13be4175cd7e95e106752e59bf66272e3a7f Wed Mar 29 14:51:26 2017 -0700

• masked sequence available refs #17435
  • src/hg/makeDb/doc/xenLae2/initialBuild.txt - lines changed 843, context: html, text, full: html, text

d9397946af9e70b18602bf975ac7fd6ea8cdbe2c Wed Mar 29 16:50:55 2017 -0700

• adding xenLae2/frog to the build refs #17435
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra - lines changed 8, context: html, text, full: html, text

5602ba37bef06187a16bbdf64740c07f72c515f5 Thu Mar 30 12:10:28 2017 -0700

• adding xenLae2 rules refs #17435
  • src/hg/makeDb/schema/all.joiner - lines changed 14, context: html, text, full: html, text

e5d119653130ef7319d517fbd9cd402fbc5146ed Thu Mar 30 12:48:21 2017 -0700

• adding gold track search rule resf #17435
  • src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra - lines changed 5, context: html, text, full: html, text

f6396fe6bbab0048bff8d20952fc4cbb06e47eef Thu Mar 30 13:50:32 2017 -0700

• adding chainNet overrides refs #14560
  • src/hg/makeDb/trackDb/frog/nanPar1/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra - lines changed 2, context: html, text, full: html, text

050b84cd063f57788bf9756b825331c7fdba6d50 Thu Mar 30 14:39:21 2017 -0700

• adjusting distances to equal the 191way refs #17545
  • src/hg/utils/phyloTrees/209way.nh - lines changed 9, context: html, text, full: html, text

9b912a13bff7b8f4066ed24e821d0592619e45c1 Thu Mar 30 15:25:49 2017 -0700

• adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
  • src/hg/utils/phyloTrees/213way.nh - lines changed 213, context: html, text, full: html, text

dff685504119eaadc1d7c1aeae0eca7499fb6cd7 Thu Mar 30 15:43:25 2017 -0700

• adding gekJap1, xenLae2, thaSir1, proMuc1 refs #17545
  • src/hg/utils/phyloTrees/213way.commonNames.nh - lines changed 213, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/213way.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/213way.scientificNames.nh - lines changed 213, context: html, text, full: html, text

a6a3a94f8e616b6ba0193cc3ffd894283e08d715 Thu Mar 30 16:22:56 2017 -0700

• Added xenLae Xenopus laevis refs #17435
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

3e681caf6447b2a59eef2ca7d0ddee3d7f9bfa15 Thu Mar 30 16:26:01 2017 -0700

• starting genbank run refs #17435
  • src/hg/makeDb/doc/xenLae2/initialBuild.txt - lines changed 101, context: html, text, full: html, text

63543032e4482a8073eeda5973dc8d47dfe218f2 Fri Mar 31 00:16:03 2017 -0700

• working through more lastz chainNet runs refs #19151
  • src/hg/makeDb/doc/xenTro9/initialBuild.txt - lines changed 200, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro9/lastzRuns.txt - lines changed 56, context: html, text, full: html, text

3510e8852c6a43c649aa82f1e62896d2820f7066 Fri Mar 31 00:17:25 2017 -0700

• running up genbank refs #17435
  • src/hg/makeDb/doc/xenLae2/initialBuild.txt - lines changed 30, context: html, text, full: html, text

89710b2afec0e248b15d4080bf114d44ce8181b2 Fri Mar 31 00:18:34 2017 -0700

• working up xenTro9 and xenLae2 lastz chainNet tracks refs #17435 #19151
  • src/hg/makeDb/doc/mm10.txt - lines changed 129, context: html, text, full: html, text

124eb6aa179a7b46d7715bf0bd1cd666c7819cd4 Fri Mar 31 00:19:52 2017 -0700

• liftover to xenTro9 refs #19151
  • src/hg/makeDb/doc/xenTro3.txt - lines changed 14, context: html, text, full: html, text

b78a4f9c10e1ba98096be2db6c352f6905d1d44e Fri Mar 31 00:20:36 2017 -0700

• liftover to xenTro9 refs #19151
  • src/hg/makeDb/doc/xenTro7.txt - lines changed 14, context: html, text, full: html, text

a056181e5d871edab02c67feb42c3951b42e808d Fri Mar 31 00:26:03 2017 -0700

• lastz chainNet runs for rhiBie1 xenTro9 xenLae2 refs #18958 #19151 #17435
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 223, context: html, text, full: html, text

29b3b8c536e52c763eaac9c322ee474c2ce06240 Fri Mar 31 00:27:30 2017 -0700

• tupChi1 done and QA Ready refs #10146
  • src/hg/makeDb/doc/tupChi1/initialBuild.txt - lines changed 24, context: html, text, full: html, text

4c3dab38b41e4385028dc2f7ee0f76c8c3c2a9f5 Fri Mar 31 00:30:32 2017 -0700

• lastz chainNet runs for galVar1 hg19 hg38 mm10 tupBel1 refs #10146
  • src/hg/makeDb/doc/tupChi1/lastzRuns.txt - lines changed 207, context: html, text, full: html, text

3a03cd6b8c2449cc1ddaa2834b5e1c77b03e796f Mon Apr 3 09:38:00 2017 -0700

• v347 final build refs #19120
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

d53b61de2752fd4bc6995101d47eaa8ab7e697aa Mon Apr 3 09:52:29 2017 -0700

• New version number v347
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text