Commits for hiram

v363_preview2 to v363_base (2018-03-19 to 2018-03-26) v363

26322399c9941a152481478073184d343637bcaf Mon Mar 19 18:37:45 2018 -0700

• add check for to/from previous version liftOvers when version > 1 no redmine
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 19, context: html, text, full: html, text

7f6db5b4eb9cf5e6e5b5fd41906b8a8de98fc9de Tue Mar 20 09:30:23 2018 -0700

• QA Ready refs #21043
  • src/hg/makeDb/doc/felCat9/initialBuild.txt - lines changed 367, context: html, text, full: html, text

4966d743257e8792a1c00561c286ec77c8ccdd6d Tue Mar 20 09:34:36 2018 -0700

• lastz chainNet for thaSir1 felCat9 and casCan1 refs #21043 #19883 #21116
  • src/hg/makeDb/doc/mm10.txt - lines changed 215, context: html, text, full: html, text

69fa55e9782319bf001fa8c36ffbe390fced3205 Tue Mar 20 09:36:41 2018 -0700

• lastz chainNet for thaSir1 felCat9 and casCan1 refs #21043 #19883 #21116
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 252, context: html, text, full: html, text

d2c809ae4d4554bed631c747bce60636cb27ef0a Tue Mar 20 09:45:17 2018 -0700

• Ensembl genes can be optional, show count of tables in optional categories refs #16028
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 26, context: html, text, full: html, text

e87f79b092f5e36115fd288fad5cea22646b4646 Tue Mar 20 10:13:02 2018 -0700

• some genbank tables are no longer required items refs #16028
  • src/hg/utils/automation/makePushQSql.pl - lines changed 34, context: html, text, full: html, text

6907e96ac2f83570458d8d4602f9a50bc4980db9 Tue Mar 20 12:15:22 2018 -0700

• QA Ready refs #16028
  • src/hg/makeDb/doc/thaSir1/initialBuild.txt - lines changed 835, context: html, text, full: html, text

104d5620c3a548f3f65b7b9e81e101c461bcbd77 Tue Mar 20 12:18:21 2018 -0700

• add blatServer check refs #16028
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 5, context: html, text, full: html, text

008c37f0b59188a483222edcb7c514e0bd8689fa Wed Mar 21 13:46:22 2018 -0700

• completed chainNet lastz runs to beaver/casCan1 refs #2116
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 7, context: html, text, full: html, text

10f796c6c24568a19fd7dc445a9ea87e8b0ade80 Wed Mar 21 14:25:23 2018 -0700

• adding Beaver casCan1 chainNet definitions refs #21116
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.euarchontoglires.ra - lines changed 53, context: html, text, full: html, text

afeecd22e96af200aa243b4334550a61570ac226 Wed Mar 21 17:03:48 2018 -0700

• adding casCan1 definitions refs #21116
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

1053ac3a46b6a3064a2cf6671627a25ff2e1e385 Wed Mar 21 18:49:08 2018 -0700

• check for chainNet on hg38 and mm10 to target db and gold search rule and all.joiner entry refs #21116
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 29, context: html, text, full: html, text

4a7c04670850782c51fd8edeacde940cf4f6a21e Wed Mar 21 19:02:07 2018 -0700

• adding NCBI RefSeq and gold/assembly search rule refs #21116
  • src/hg/makeDb/trackDb/mammal/casCan1/trackDb.ra - lines changed 7, context: html, text, full: html, text

76b7570610850b5d46c0f620664aa78d969d2f96 Wed Mar 21 21:31:07 2018 -0700

• QA Ready refs #21116
  • src/hg/makeDb/doc/casCan1/initialBuild.txt - lines changed 269, context: html, text, full: html, text

a208b6494eb8e9dfde4d24e3ab8364931fce6bab Thu Mar 22 09:55:14 2018 -0700

• adding neoSch1 Monk seal chainNet definitions refs #19883
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra - lines changed 55, context: html, text, full: html, text

6bfc2469cc844e0e9674a1b42f03fb9080bdd463 Thu Mar 22 12:44:45 2018 -0700

• adding NCBI RefSeq composite include refs #19883
  • src/hg/makeDb/trackDb/seal/neoSch1/trackDb.ra - lines changed 2, context: html, text, full: html, text

2396e45154fb57b93e7988d5f00efc2d64bbbcb9 Thu Mar 22 12:49:25 2018 -0700

• move the RBest and Syntenic chainNets to optional list and avoid hg38 and mm10 self checks refs #19883
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 40, context: html, text, full: html, text

04304727abc7186de4c1f5491a856d78398d4b0a Thu Mar 22 14:20:09 2018 -0700

• recognize tables in a track type psl refs #19883
  • src/hg/utils/automation/makePushQSql.pl - lines changed 14, context: html, text, full: html, text

e3dec7ffbb0614d2796e0706b2313f7ea7849e3e Thu Mar 22 14:34:53 2018 -0700

• completed neoSch1 QA Ready refs #19883
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/neoSch1/initialBuild.txt - lines changed 124, context: html, text, full: html, text

b8303f22da89371b05a46134dfddbb3e9515c408 Fri Mar 23 10:27:55 2018 -0700

• better error message from axtChain when 2bit or nib arguments do not exist refs #20928
  • src/hg/mouseStuff/axtChain/axtChain.c - lines changed 4, context: html, text, full: html, text
  • src/inc/portable.h - lines changed 3, context: html, text, full: html, text
  • src/lib/osunix.c - lines changed 11, context: html, text, full: html, text

c3bb5a0e0757e2f66a06395b05fc78a7f2957e87 Fri Mar 23 11:34:33 2018 -0700

• manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 12, context: html, text, full: html, text

1b1678cabcf7065d8c7e82da019cdcdd074570e8 Fri Mar 23 11:45:00 2018 -0700

• manage dataVersion trackDb setting in conjuction with hgFixed.trackVersion table refs #20215
  • src/hg/inc/hui.h - lines changed 6, context: html, text, full: html, text

9d07cef01b2d3acd8c1d030faf43f7f10604db8e Sat Mar 24 08:24:59 2018 -0700

• adding panTro6 to the browser refs #20979
  • src/hg/makeDb/trackDb/chimp/panTro6/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/gold.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/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

8a5fa10564b53cc6f586b5506a5956b1ddd559aa Sat Mar 24 08:35:15 2018 -0700

• add gold/assembly search rule and include NCBI RefSeq composite refs #20979
  • src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra - lines changed 7, context: html, text, full: html, text

a4e273160689f332baa2138d7cb06419af9c0550 Sat Mar 24 22:04:42 2018 -0700

• adding panTro6 chainNet definitions refs #20979
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 53, context: html, text, full: html, text

3e7d2e3f6fc6b0e8c12a0b5daf10d4cdc7f73b21 Sat Mar 24 22:06:03 2018 -0700

• running up lastz chainNet to mm10 and hg38 refs #20979
  • src/hg/makeDb/doc/panTro6/initialBuild.txt - lines changed 968, context: html, text, full: html, text

672c01f6a8c31818c4e5dd061161b511068305f9 Sat Mar 24 22:09:16 2018 -0700

• adding panTro6 rules refs #20979
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text

6a70196500cdf94ac6218c9ee739511b65e6d657 Sun Mar 25 14:35:27 2018 -0700

• adding panTro6 to the system refs #20979
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 2, context: html, text, full: html, text

611e96cad657e7efb518aab3ac07c7d514d9e3dc Sun Mar 25 14:45:22 2018 -0700

• lastz chaiNet done to mm10 and hg38 refs #20979
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro6/initialBuild.txt - lines changed 200, context: html, text, full: html, text

dcb5f4e014a749344101c180eb667341effd4432 Sun Mar 25 23:28:27 2018 -0700

• adding ponAbe3 browser refs #20980
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra - lines changed 8, context: html, text, full: html, text

7e09c0dfe844a7e624aa2a1c6e4ab0dbb498f2bd Mon Mar 26 10:03:59 2018 -0700

• v363 final build refs #21106
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

987435c6cae84cc8cfbda95139d31f645fb7ca43 Mon Mar 26 10:06:31 2018 -0700

• running repeatMasker windowMasker refs #20980
  • src/hg/makeDb/doc/ponAbe3/initialBuild.txt - lines changed 1006, context: html, text, full: html, text

b7539ba8ad8a6148ebd8232baeaab4d6730898f6 Mon Mar 26 10:07:38 2018 -0700

• table exists if 1 or more columns and make the RBest and Syntenic tracks optional on mm10 and hg38 refs #21128
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 19, context: html, text, full: html, text

19333f51986cd07483a290b548d9624df0ccd4b6 Mon Mar 26 10:09:04 2018 -0700

• crispr build broken at last step refs #20540
  • src/hg/makeDb/doc/criGriChoV2/initialBuild.txt - lines changed 30, context: html, text, full: html, text

bfaf5bb6d1667d2d9faef2cc9d3fbbac012b730c Mon Mar 26 10:09:51 2018 -0700

• liftOver to felCat9 refs #21043
  • src/hg/makeDb/doc/felCat5.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/felCat8/initialBuild.txt - lines changed 14, context: html, text, full: html, text

038d205f7fdf28afaed7f5dc27b04f31628cf9a3 Mon Mar 26 10:10:58 2018 -0700

• attempting to run up tandemDups having much difficulty refs #9870
  • src/hg/makeDb/doc/ficAlb1/initialBuild.txt - lines changed 17, context: html, text, full: html, text

1e2f999205030c61a3b9999fab726875af577546 Mon Mar 26 10:12:13 2018 -0700

• running up a 3-way multiple alignment no redmine
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 1365, context: html, text, full: html, text

a8ef7d52b32a22999c95967270a8fb4eda3b321e Mon Mar 26 10:12:53 2018 -0700

• liftOver to panTro6 refs #20979
  • src/hg/makeDb/doc/panTro5/initialBuild.txt - lines changed 13, context: html, text, full: html, text

3753975cb92612394220ce12cdd30ad429736938 Mon Mar 26 10:14:09 2018 -0700

• some extra verbose(3) for debugging no redmine
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 9, context: html, text, full: html, text

22c0beb9c98122cfc85aed0b561fab682a26d8c4 Mon Mar 26 10:14:48 2018 -0700

• adding tantan repeat track experiment no redmine
  • src/hg/makeDb/trackDb/tantan.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 7, context: html, text, full: html, text

7f9a26caa49ff5bea1f9791e8513b94c6587d3e6 Mon Mar 26 10:15:57 2018 -0700

• adding American beaver Castor canadensis refs #21116
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 3, context: html, text, full: html, text

7dc72516c18322453473dc52a2eab5de480e297a Mon Mar 26 10:17:05 2018 -0700

• add static to lowerToN() function to avoid conflict with same named function in library noticed by Encode DCC user no redmine
  • src/utils/faLowerToN/faLowerToN.c - lines changed 1, context: html, text, full: html, text

a97dcf79cc86cb79231374f6250927a360b03645 Mon Mar 26 10:19:40 2018 -0700

• New version number v363
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text