Commits for hiram

v360_preview to v360_preview2 (2018-01-08 to 2018-01-16) v360

14971a27bce60ec145d4dec1fb0b09f249511a76 Mon Jan 8 10:38:44 2018 -0800

• crispr10K tracks can now be seen on ce10 hbv1 mm10 staAur1 anoGam3 refs #0743
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 2, context: html, text, full: html, text

714ffecbab169fb2467b47a323995f95d0b97706 Mon Jan 8 13:30:57 2018 -0800

• adding ensGene and crispr10K tracks refs #20743
  • src/hg/makeDb/doc/anoGam3/initialBuild.txt - lines changed 246, context: html, text, full: html, text

4ecbbeb768fa003f3164f0a014ecccf144268c13 Mon Jan 8 18:43:57 2018 -0800

• adding ficAlb1 - Ficedula albicollis - collard flycatcher refs #9870
  • 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

73e75eccb6cba0a17ae7abb221148d409bc75751 Mon Jan 8 18:56:45 2018 -0800

• adding papAnu4 Papio anubis - olive baboon refs #20769
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text

5a92b3984d39408749b1ed37045e810b17c5ee65 Mon Jan 8 22:15:17 2018 -0800

• adding criGriChoV2 Cricetulus griseus cell line CHO-K1 refs #20540
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

70282bf14f8a7b30dea908c56fc61cad7279d4ad Mon Jan 8 22:38:02 2018 -0800

• adding cavApe1 Cavia aperea Brizilian guinea pig refs #20770
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

23910020e89fc566f43bbfdfd06552454b221380 Tue Jan 9 09:37:02 2018 -0800

• adding ficAlb1 to the update alignments refs #9870
  • 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

e4e5325b502ebed2dc000fcb28c69cbcb262c78f Tue Jan 9 10:29:31 2018 -0800

• fixing pathnames for cavApe1 refs #20770
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 2, context: html, text, full: html, text

a89bfe4906e124c5d6a0c7dd188650c56a5036a9 Tue Jan 9 10:35:14 2018 -0800

• adding papAnu4 to the update alignments refs #20769
  • 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

37b32f1e7817dcbe7de7d5aa097912a90c9b71a6 Tue Jan 9 14:34:37 2018 -0800

• adding cavApe1 to the update alignments refs #20770
  • 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

dd9925b1305828b4c2a608bb07675794b1f03047 Tue Jan 9 21:41:09 2018 -0800

• adding criGriChoV2 to the update alignments refs #20540
  • 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

950db5b87a30a254b67c01855de3ee8816ace145 Wed Jan 10 10:59:30 2018 -0800

• run up lastz/chainNet for criGriChoV2 papAnu4 cavApe1 ficAlb1 and panTro3 on hg38 refs #20540 #20769 #20770 #9870 #17504
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 388, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 260, context: html, text, full: html, text

83d406ebfff2ffad31502f8fac3e681cf258fd75 Wed Jan 10 11:18:04 2018 -0800

• adding rules for ficAlb1 cavApe1 criGriChoV2 papAnu3 refs #9870 #20770 #20540 #20759
  • src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text

bc7564d8e57ba1bb89a3292efbcbc3139c90cd5d Wed Jan 10 17:15:53 2018 -0800

• to catch up with Ensembl release v91, QA Ready refs #20770
  • src/hg/makeDb/doc/cavApe1/initialBuild.txt - lines changed 954, context: html, text, full: html, text

0db946ddc862c388b463902ced3eaf0f050d3a49 Wed Jan 10 17:19:27 2018 -0800

• attempt catch with Ensembl release v91 but their release was a much older sequence refs #9870
  • src/hg/makeDb/doc/ficAlb1/initialBuild.txt - lines changed 131, context: html, text, full: html, text

caf7f66a080240cb343e9e9dabd628f0e6b97fbc Wed Jan 10 17:23:47 2018 -0800

• catching up to Ensembl v91 release refs #20540
  • src/hg/makeDb/doc/criGriChoV2/initialBuild.txt - lines changed 317, context: html, text, full: html, text

5aeeb014a98558fefa023f237abd29f02d8ae42d Wed Jan 10 17:27:04 2018 -0800

• catching up to Ensembl release v91 refs #20769
  • src/hg/makeDb/doc/papAnu4/initialBuild.txt - lines changed 135, context: html, text, full: html, text

26286f426d7cd5922e2d1e4d098b4cf2a6f55397 Wed Jan 10 17:28:20 2018 -0800

• remove trailing blanks refs #20770
  • src/hg/makeDb/doc/cavApe1/initialBuild.txt - lines changed 1, context: html, text, full: html, text

71f07bcffb4709109d882b2faac5d1811e34040a Thu Jan 11 11:26:32 2018 -0800

• adding cavApe1 and fukDam1 Brazilian guinea pig and Damara mole-rat refs #20770 #20752
  • src/hg/js/dbDbTaxonomy.js - lines changed 11, context: html, text, full: html, text

b574473817079811671096b5cb7fb219530be5dc Thu Jan 11 11:31:56 2018 -0800

• update notes during update 2018-01-11 no redmine
  • src/hg/makeDb/doc/dbDbTaxonomy.txt - lines changed 12, context: html, text, full: html, text

9c9e11889ba3abf8287c56c5909b5695ab6edf44 Thu Jan 11 11:32:49 2018 -0800

• liftOver to anoGam3 refs #20743
  • src/hg/makeDb/doc/anoGam1.txt - lines changed 18, context: html, text, full: html, text

631e141c2d368e654de036bc4bd82802ceed6483 Thu Jan 11 11:33:28 2018 -0800

• correct defaultPosition refs #20770
  • src/hg/makeDb/doc/cavApe1/initialBuild.txt - lines changed 1, context: html, text, full: html, text

c6e704da62c47b77a828cd8c09f64234c6521b5b Thu Jan 11 11:34:16 2018 -0800

• genomewiki page for 6-way alignment no redmine
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 5, context: html, text, full: html, text

f4fc51970f35afcba95e138ba7ffbf39e36d9673 Thu Jan 11 11:36:12 2018 -0800

• liftOver to dipOrd2 refs #20751
  • src/hg/makeDb/doc/dipOrd1.txt - lines changed 15, context: html, text, full: html, text

252fbe2630ffc34ba67275a78039176a8765f80f Thu Jan 11 11:37:04 2018 -0800

• chainNet to anoGam3 refs #20743
  • src/hg/makeDb/doc/dm6.txt - lines changed 67, context: html, text, full: html, text

ef33c3732a399ef285ce299e8c3bafb1aa360722 Thu Jan 11 11:37:57 2018 -0800

• genomewiki status pages for 6-way alignment no redmine
  • src/hg/makeDb/doc/galVar1/multiz6way.txt - lines changed 5, context: html, text, full: html, text

b0ee4c4ea80e5f0f1b7d2284d9463fd54303222d Thu Jan 11 11:38:16 2018 -0800

• genomewiki status pages for 5-way alignment no redmine
  • src/hg/makeDb/doc/hg38/multiz5way.txt - lines changed 5, context: html, text, full: html, text

df7fc755086b35477a73c87463b50ecf33d5b956 Thu Jan 11 11:39:00 2018 -0800

• liftOver to papAnu4 refs #20769
  • src/hg/makeDb/doc/papAnu2.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/papAnu3/initialBuild.txt - lines changed 14, context: html, text, full: html, text

5ed2d4a3edd913536da9faca9418ae1a54d05cb6 Thu Jan 11 11:39:38 2018 -0800

• genomewiki status page for 5-way no redmine
  • src/hg/makeDb/doc/tupChi1/multiz5way.txt - lines changed 1, context: html, text, full: html, text

b1b355ce357e00c4eb84739db8f75b95bb078631 Thu Jan 11 11:40:55 2018 -0800

• adding ensGene override for URL to metazoa.ensembl.org refs #20743
  • src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra - lines changed 4, context: html, text, full: html, text

65a60bdc792a12cd342e719fe38ab0f9975d797b Thu Jan 11 11:43:10 2018 -0800

• no longer needed definitions have been included in other subsets no redmine
  • src/hg/makeDb/trackDb/human/chainNetLegacy.ra - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetStray.ra - lines changed 14, context: html, text, full: html, text

18fa4aa598e9f71be0e1723ba3b9570f74b52277 Thu Jan 11 11:43:35 2018 -0800

• no longer needed definitions have been included in other subsets no redmine
  • src/hg/makeDb/trackDb/human/newChainNet.ra - lines changed 322, context: html, text, full: html, text

5baca4fd235d872d4c522ffae9fe26ca9fde341b Thu Jan 11 13:46:51 2018 -0800

• better, more restricted, search termRegex for the gold track to prevent excessive results refs #20770 #20809
  • src/hg/makeDb/trackDb/guineaPig/cavApe1/trackDb.ra - lines changed 1, context: html, text, full: html, text

08c5217ebf53c216f38a9fb641e9b9f601c3946e Fri Jan 12 14:34:21 2018 -0800

• initial set of files refs #20819
  • src/hg/makeDb/trackDb/lamprey/petMar3/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar3/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar3/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar3/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

4ebd38aaf09a2db1fdbfebad9cc76cae7a2fe9f9 Fri Jan 12 14:55:44 2018 -0800

• new dependent crispr10K.ra file for trackDb build refs #20819
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text

8d080e8275a37ec089274051eb92266cf4072faf Fri Jan 12 16:27:39 2018 -0800

• adding gold table assembly track search rule refs #20819
  • src/hg/makeDb/trackDb/lamprey/petMar3/trackDb.ra - lines changed 5, context: html, text, full: html, text

8d346ba47a6fbec178c8b28f39c2aaed395696dd Fri Jan 12 21:17:47 2018 -0800

• adding petMar3 - Petromyzon marinus - lamprey refs #20819
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text

26c5373d5731d708c0417e81c17d241be3f85c11 Fri Jan 12 22:01:14 2018 -0800

• running up genbank, liftOvers refs #20819
  • src/hg/makeDb/doc/petMar3/initialBuild.txt - lines changed 836, context: html, text, full: html, text

6cc89b471714794f170e8e327beda78516d58e5f Tue Jan 16 09:56:53 2018 -0800

• v360 preview2
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text