Commits for hiram

v359_base to v360_preview (2017-12-18 to 2018-01-08) v360

c99090b56ef946bbfe6beb4e9c2d428f8abad935 Mon Dec 18 13:47:18 2017 -0800

• multiple alignments enough done for a look see no redmine
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/galVar1/multiz6way.txt - lines changed 1490, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/multiz5way.txt - lines changed 1464, context: html, text, full: html, text
  • src/hg/makeDb/doc/tupChi1/multiz5way.txt - lines changed 1471, context: html, text, full: html, text

40b1280bc13ea274af99b4434a6af798a5405e64 Mon Dec 18 14:29:34 2017 -0800

• adding 5-way mammal alignment no redmine
  • src/hg/makeDb/trackDb/human/hg38/cons5way.html - lines changed 438, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.5way.ra - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

ddf2311e413ff8c66180f54fbc29aa5013a761d1 Mon Dec 18 14:44:11 2017 -0800

• 6-way alignment phylo tree for galVar1 no redmine
  • src/hg/htdocs/images/phylo/galVar1_6way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

940a472493cada80db6f3cdf904317203ea841cb Mon Dec 18 14:46:10 2017 -0800

• adding 6-way alignment no redmine
  • src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html - lines changed 433, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.6way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra - lines changed 2, context: html, text, full: html, text

422ac9b87674259386ff82324f8643d4cb7ca147 Mon Dec 18 14:51:35 2017 -0800

• 5-way alignment tree for tupChi1 no redmine
  • src/hg/htdocs/images/phylo/tupChi1_5way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

ac1837db78e0e3c82532a32503901e232b4bf551 Mon Dec 18 14:52:59 2017 -0800

• adding 5-way alignment no redmine
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html - lines changed 427, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.5way.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra - lines changed 1, context: html, text, full: html, text

3414b871c08ab28abffc0d5b00cc95e153ae13e0 Mon Dec 18 15:06:52 2017 -0800

• updated text no redmine
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html - lines changed 18, context: html, text, full: html, text

68813efac90f262c8cf21dc23902820af1e969d5 Tue Dec 19 11:46:42 2017 -0800

• correct assembly accession ID no redmine
  • src/hg/makeDb/trackDb/human/hg38/description.html - lines changed 2, context: html, text, full: html, text

b059002aee613e7743d7eacdfbd2717701f5eb64 Tue Dec 19 14:31:46 2017 -0800

• begin anoGam3 browser build no redmine
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 753, context: html, text, full: html, text

3adcb0ff38e58b30dc4981b250c7a86295fcb286 Tue Dec 19 15:24:43 2017 -0800

• initial files for anoGam3 no redmine
  • src/hg/makeDb/trackDb/anopheles/anoGam3/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/anopheles/anoGam3/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/anopheles/anoGam3/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

31fa3dbc54d190496af806c94008a2b82af5e7c0 Tue Dec 19 15:54:07 2017 -0800

• add gold table search rule no redmine
  • src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra - lines changed 5, context: html, text, full: html, text

0c717a44adcac01499ad89f893a48a0865be7fe4 Tue Dec 19 16:17:10 2017 -0800

• continuing with RepeatMasker
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 251, context: html, text, full: html, text

50f490d8d606e9b72e92da2e42753fe817917265 Wed Dec 20 08:11:45 2017 -0800

• Added anoGam3; no redmine
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

c44f0ad0ae624dbff869c4d89b552417bec5dd8c Wed Dec 20 15:36:24 2017 -0800

• improved procedure to allow duplicates from other names to same UCSC name refs #20696
  • src/hg/utils/automation/chromAlias.pl - lines changed 125, context: html, text, full: html, text

6535b146f2e677145a09721b4a4ce74efff7028a Wed Dec 20 15:51:27 2017 -0800

• adding anoGam3 chainNet no redmine
  • src/hg/makeDb/trackDb/trackDb.chainNet.insects.ra - lines changed 54, context: html, text, full: html, text

8a65d0697c43d24e5add86d1921523beec1760c4 Wed Dec 20 18:02:46 2017 -0800

• waiting for genbank run to finish refs #20743
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 211, context: html, text, full: html, text

f858434bab25856f342151b173813d2f6e2b7668 Wed Dec 20 20:06:09 2017 -0800

• adding rules for anoGam3 refs #20743
  • src/hg/makeDb/schema/all.joiner - lines changed 23, context: html, text, full: html, text

393adbd5597ac296698ee21c3a4f2d6a431a7ba9 Thu Dec 21 08:24:00 2017 -0800

• Added anoGam3 - malaria mosquito refs #20743
  • 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

77623908c6e6655852cf957a2ff956295de4f617 Thu Dec 21 08:25:52 2017 -0800

• photo for anoGam3 refs #20743
  • src/hg/htdocs/images/Anopheles_gambiae.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

4969685a0d16a10c689d921e87281ae0a06320bc Thu Dec 21 09:57:14 2017 -0800

• QA ready refs #20743
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 66, context: html, text, full: html, text

abdaf2d94220c3ea7c63a314e0897e74dd740eb6 Thu Dec 21 10:00:22 2017 -0800

• reset base position refs #20743
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 9, context: html, text, full: html, text

4fcbf3c4cd85f278e97c708c11d7f695cbfdf6f3 Fri Dec 22 21:39:42 2017 -0800

• adding dipOrd2 to the build refs #20751
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd2/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd2/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 2, context: html, text, full: html, text

f2b2b152a855f138e0660bfbb1f3147c5d29744b Fri Dec 22 21:47:36 2017 -0800

• add gold table search rule refs #20751
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd2/trackDb.ra - lines changed 5, context: html, text, full: html, text

92fba655e042b9abfb9f74626895aaed04338607 Fri Dec 22 21:48:30 2017 -0800

• correctly dipOrd2 refs #20751
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

2696cff97946f81916d21b644f50018c62a8a2d3 Fri Dec 22 21:54:23 2017 -0800

• begin dipOrd2 build refs #20751
  • src/hg/makeDb/doc/dipOrd2/initialBuild.txt - lines changed 774, context: html, text, full: html, text

2212307d88c8d8d050d9c64d5e6d437f6fc22243 Fri Dec 22 22:01:53 2017 -0800

• liftOver from hg11 to hg19 and hg38 refs #20736
  • src/hg/makeDb/doc/hg11.txt - lines changed 35, context: html, text, full: html, text

e019404e7b790e98793dd363f984ac5346dfd203 Fri Dec 22 23:43:59 2017 -0800

• add fukDam1 to the build refs #20752
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mammal/fukDam1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mammal/fukDam1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mammal/fukDam1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mammal/fukDam1/trackDb.ra - lines changed 8, context: html, text, full: html, text

d83b17b1b9578f9278801befc40b9cc421670514 Sat Dec 23 00:02:12 2017 -0800

• adding gold track search rule refs #20752
  • src/hg/makeDb/trackDb/mammal/fukDam1/trackDb.ra - lines changed 5, context: html, text, full: html, text

41e7bfe29214a6018767d8a297cd5e9b00e010f0 Sun Dec 31 08:54:37 2017 -0800

• adding dipOrd2 Dipodomys ordii refs #20751
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

1739294775fb13c71d448f26e9e79afd9411157f Sun Dec 31 15:04:58 2017 -0800

• adding fukDam1 - Fukomys damarensis - Damara mole-rat refs #20752
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

c2c870d22d20a0caa44aa498fea09cd985cae5d3 Mon Jan 1 19:57:04 2018 -0800

• adding fukDam1 and dipOrd2 to the update alignments refs #20752 #20751
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 3, context: html, text, full: html, text

ac9a56fb921dfb228a34119dc2f0bc87cbeda2e2 Tue Jan 2 12:00:43 2018 -0800

• adding fukDam1 and dipOrd2 chainNet refs #20751 #29752
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 251, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra - lines changed 106, context: html, text, full: html, text

bc3d13133e1265d493c24dff6bcd63fa0bdc808f Wed Jan 3 10:18:10 2018 -0800

• adding fukDam1 and dipOrd2 rules refs #20752 #20751
  • src/hg/makeDb/schema/all.joiner - lines changed 6, context: html, text, full: html, text

61ccc644d4988c210f98c5de776a3de7a5fe6c7a Wed Jan 3 10:29:08 2018 -0800

• lastz/chainNet to fukDam1 and dipOrd2 refs #20751 #20752
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 158, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 129, context: html, text, full: html, text

39cc657b345aad224493b760e875f4f95a356b68 Wed Jan 3 11:47:10 2018 -0800

• browser is QA Ready refs #20752
  • src/hg/makeDb/doc/fukDam1/initialBuild.txt - lines changed 804, context: html, text, full: html, text

84ee80e78bb063ee24c602adca839d51504e2dca Wed Jan 3 11:51:35 2018 -0800

• browser is QA Ready refs #20751
  • src/hg/makeDb/doc/dipOrd2/initialBuild.txt - lines changed 329, context: html, text, full: html, text

30689fbfc5863fcbc71712b0c0279e604d6b2b31 Wed Jan 3 15:10:29 2018 -0800

• was not recognizing the genbank accession ID and renameMySQLCommonName variable refs #20540 #20722
  • src/hg/utils/automation/prepConfig.pl - lines changed 13, context: html, text, full: html, text

c7354491a93371f7ed5e605b6c2eaad847689982 Wed Jan 3 16:53:45 2018 -0800

• initial files for criGriChoV2 refs #20540
  • src/hg/makeDb/trackDb/criGri/criGriChoV2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV2/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra - lines changed 8, context: html, text, full: html, text

df53a7fa312a6fa984417047d0ace7c9ee2c4941 Wed Jan 3 17:42:37 2018 -0800

• adding papAnu4 to the build refs #20768
  • src/hg/makeDb/trackDb/baboon/papAnu4/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu4/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu4/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

98925e2605ed8669d0e88fca346ebfeded675efa Wed Jan 3 17:47:57 2018 -0800

• running up repeatMasker and simpleRepeat refs #20769
  • src/hg/makeDb/doc/papAnu4/initialBuild.txt - lines changed 818, context: html, text, full: html, text

1b2ecf649edc6355b87bd0a5f6fb646599469c5d Wed Jan 3 17:48:28 2018 -0800

• running up repeatMasker and simpleRepeat refs #20540
  • src/hg/makeDb/doc/criGriChoV2/initialBuild.txt - lines changed 788, context: html, text, full: html, text

a512688e18eb437953bf87bfc331bdb3f3b000d7 Wed Jan 3 22:17:42 2018 -0800

• updating to new browser versions no redmine
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 7, context: html, text, full: html, text

67fe54da819ba950c79fe57ef80494e1f53820e5 Thu Jan 4 10:12:53 2018 -0800

• phot from flickr www.flickr.com/photos/trekman/4712570295 Gustavo Fernando Durán
  • src/hg/htdocs/images/Cavia_aperea.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

1200278b75d93b425005aab6d5c0b2224dcd72b8 Thu Jan 4 11:52:49 2018 -0800

• masking done, continuing build refs #20540
  • src/hg/makeDb/doc/criGriChoV2/initialBuild.txt - lines changed 67, context: html, text, full: html, text

e6c4b8dff40a054bb6e302c6b606377fe9358a29 Thu Jan 4 13:40:23 2018 -0800

• adding cavApe1 to the build and turn on criGriChoV1 criGriChoV2 refs #20770 #20540 #19228
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 3, context: html, text, full: html, text

71fced743cd036e9a9a1295dcf376fc335097be4 Thu Jan 4 15:34:32 2018 -0800

• add assembly track search rule refs #20770
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra - lines changed 5, context: html, text, full: html, text

a42a7cedfcc556c6f202a11483fd3dc3e3f9218f Fri Jan 5 10:00:26 2018 -0800

• fix error when one of the inputs only has one line refs #20540
  • src/hg/utils/automation/chromAlias.pl - lines changed 2, context: html, text, full: html, text

290b86d4a2936265c8cb6162bf13df521439b988 Fri Jan 5 10:06:45 2018 -0800

• add assembly track search rule refs #20540
  • src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra - lines changed 5, context: html, text, full: html, text

7069b166edb308a0707ecee7cdc5bad852085ceb Fri Jan 5 10:36:22 2018 -0800

• fixup one of the path names for peptides criGriChoV2 refs #20696
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1, context: html, text, full: html, text

36f7d91fe577f89a5d3a1cb62c40c5483010bfd3 Fri Jan 5 10:41:56 2018 -0800

• fixup one of the path names for peptides criGriChoV2 refs #20696
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1, context: html, text, full: html, text

b2852526011bd97e06679d7659b94715a650f029 Fri Jan 5 13:27:06 2018 -0800

• add assembly track search rule refs #20769
  • src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra - lines changed 5, context: html, text, full: html, text

844a643864852f43bd1033c8fda3c7c59bdfc28c Fri Jan 5 14:58:47 2018 -0800

• add type bigWig with limits for all the bw files refs #19154
  • src/hg/makeDb/trackDb/human/hg38/hoffMap.ra - lines changed 10, context: html, text, full: html, text

5c7b0ddad4939219f31e57b77bdb2d435bd5b119 Fri Jan 5 15:17:06 2018 -0800

• type bigWig for the composite allows the schema page to display refs #19154
  • src/hg/makeDb/trackDb/human/hg38/hoffMap.ra - lines changed 2, context: html, text, full: html, text

3db3e255262bff62cd95d693dc3b4ce0678aa958 Fri Jan 5 15:55:12 2018 -0800

• adding ficAlb1 Collared Flycatcher to the browser refs #9870
  • src/hg/makeDb/trackDb/birds/ficAlb1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/ficAlb1/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/ficAlb1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/ficAlb1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

496dc581888967a547d75db1a0d109962d788e63 Fri Jan 5 16:01:52 2018 -0800

• add assembly track search rule refs #9870
  • src/hg/makeDb/trackDb/birds/ficAlb1/trackDb.ra - lines changed 5, context: html, text, full: html, text

066deef16280ed7c0e6b58bf0d9c39a79cb5fc68 Fri Jan 5 16:03:10 2018 -0800

• ready to work up genbank run refs #9870
  • src/hg/makeDb/doc/ficAlb1/initialBuild.txt - lines changed 868, context: html, text, full: html, text

df9e377a17f4ad508c8c1bc547704c37a025110d Fri Jan 5 16:28:15 2018 -0800

• ready to run up genbank refs #20769
  • src/hg/makeDb/doc/papAnu4/initialBuild.txt - lines changed 155, context: html, text, full: html, text

ebfcb94f9b285ca27980668bbbd2569e77cb31e5 Sat Jan 6 17:16:49 2018 -0800

• new gold table new assembly track search rule refs @20770
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra - lines changed 1, context: html, text, full: html, text

8f20120f8b5c935f3e0778a79de672b53f011888 Sat Jan 6 20:40:41 2018 -0800

• rename ficAlb1 to ficAlb0 for v91 refs #20696
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 3, context: html, text, full: html, text

7af7775c43dd5ae71f939ad98203d199106126da Sat Jan 6 20:49:06 2018 -0800

• liftOver to criGriChoV2 refs #20540
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 14, context: html, text, full: html, text

1a2688ea3df2d63117cfb99e4127c6054accfd1e Sat Jan 6 20:50:50 2018 -0800

• liftOver to criGriChoV2 refs #20540
  • src/hg/makeDb/doc/criGri1.txt - lines changed 14, context: html, text, full: html, text

b3e9b8d78ae15ea27833b19d30045b171d954a67 Mon Jan 8 10:20:28 2018 -0800

• v360 preview1
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text