Commits for hiram

v346_preview to v346_preview2 (2017-02-27 to 2017-03-06) v346

64b49d1b1d01376e06772754ac94d4b802cd1c3e Mon Feb 27 10:27:02 2017 -0800

• add augustusGene build procedure refs #14437
  • src/hg/makeDb/doc/nasLar1/initialBuild.txt - lines changed 13, context: html, text, full: html, text

a598020325c86675e7fe212493fa1f150b0aada6 Mon Feb 27 11:14:27 2017 -0800

• Added macNem1; refs #18927
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

92f13b481d2017d01d64daaa69c6caefef939867 Mon Feb 27 13:09:35 2017 -0800

• indicate what happend with lastz gorGor and add chromAlias table refs #16036
  • src/hg/makeDb/doc/panPan2/initialBuild.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/panPan2/lastzRuns.txt - lines changed 2, context: html, text, full: html, text

2155f55ea01c48f279fffc5d2aba9027eff7e39d Mon Feb 27 13:37:45 2017 -0800

• adding macNem1 rules refs #18927
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

7e7c8cb7221ae305e6fa2454f5377b15ffb2c4f6 Tue Feb 28 10:33:54 2017 -0800

• (C) Copyright Jacky Poon, all rights reserved - http://www.jackypoon.org/mystery-monkeys
  • src/hg/htdocs/images/Rhinopithecus_bieti.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

68742ea2dbdb41a5130aa078aeb13993b8b66837 Tue Feb 28 14:28:41 2017 -0800

• rhiBie1 - black snub-nosed monkey - Rhinopithecus bieti refs #18958
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/trackDb.ra - lines changed 8, context: html, text, full: html, text

4d1ef500be04d162afa23585bdd663a504fc7ae1 Tue Feb 28 14:33:15 2017 -0800

• beginning build for rhiBie1 refs #18958
  • src/hg/makeDb/doc/rhiBie1/initialBuild.txt - lines changed 744, context: html, text, full: html, text

f50a54ddd5728460bd8dd33a5fccd6fa3e84eef6 Wed Mar 1 12:25:33 2017 -0800

• correct colors on scaffold names when in chain tracks refs #18656
  • src/hg/hgTracks/simpleTracks.c - lines changed 3, context: html, text, full: html, text

32ac8a3e93bdbc7e8c9cfaabb45be61a84b9c197 Wed Mar 1 14:30:47 2017 -0800

• adding lastz chain net for macNem1 and colAng1 refs #17545 #18927
  • src/hg/makeDb/doc/mm10.txt - lines changed 128, context: html, text, full: html, text

484f89767f9ad8a920db835d18f90bc98ac77ea7 Wed Mar 1 14:54:58 2017 -0800

• add chainNet for macNem1 rhiBie1 colAng1 refs #18927 #18958 #17545
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 160, context: html, text, full: html, text

ed8ae5d1bd6e510a54ce663301c67fbedbca990a Wed Mar 1 15:34:51 2017 -0800

• Added rhiBie1; refs #18958
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

d5097d97a30fb5771534e424f2ea3fec6dc1f34b Thu Mar 2 10:01:52 2017 -0800

• add search rule for gold track refs #18958
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/trackDb.ra - lines changed 5, context: html, text, full: html, text

10c4006f6c96cefd3c4fd870e91a218611e9d7e8 Thu Mar 2 10:03:29 2017 -0800

• ready for genbank run refs #18958
  • src/hg/makeDb/doc/rhiBie1/initialBuild.txt - lines changed 177, context: html, text, full: html, text

e8027ca1779ef10a8358fdd01dd4cab311fd2332 Thu Mar 2 11:30:24 2017 -0800

• adding trackDb.chainNet.ra overrides for assemblies in the rn6 20-way refs #18656
  • src/hg/makeDb/trackDb/cat/felCat8/trackDb.chainNet.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/trackDb.chainNet.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.chainNet.ra - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.chainNet.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.chainNet.ra - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/trackDb.chainNet.ra - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/trackDb.ra - lines changed 2, context: html, text, full: html, text

7f3efddb472b5ebbe47532424b65ce293c92af96 Thu Mar 2 11:40:13 2017 -0800

• script to add chainNet override trackDb entries refs #18656
  • src/hg/utils/automation/addScores.pl - lines changed 48, context: html, text, full: html, text

dee5ba96ef4b1037785e606132aec623f521e12f Thu Mar 2 14:07:38 2017 -0800

• adding micMur3 to the build refs #18984
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/trackDb.ra - lines changed 8, context: html, text, full: html, text

f3036445231924a66d82ccf888212adca93f0060 Thu Mar 2 14:24:48 2017 -0800

• new trackDb.chainNet.ra up to date with everything refs #18656
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra - lines changed 195, context: html, text, full: html, text

dee1684115f2dfea4e154de809fa9844aa8c67a7 Thu Mar 2 14:36:36 2017 -0800

• correct release tags for all chain nets in monDom5 refs #18656
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.laurasiatheria.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra - lines changed 5, context: html, text, full: html, text

253b4ed65baa32bbe58c399a4fda94916c9ac928 Thu Mar 2 14:39:43 2017 -0800

• starting micMur3 browser build refs #18984
  • src/hg/makeDb/doc/micMur3/initialBuild.txt - lines changed 748, context: html, text, full: html, text

af0fc1c89e45db46dfd76d1637ad02b68f5dad6e Thu Mar 2 15:17:14 2017 -0800

• fixup standard list of infrastructure tables refs #17545
  • src/hg/utils/automation/makePushQSql.pl - lines changed 8, context: html, text, full: html, text

a2f718591b34d7d49f661232ace1172be6e004a7 Thu Mar 2 15:35:12 2017 -0800

• colAng1 in the pushQ refs #17545
  • src/hg/makeDb/doc/colAng1/initialBuild.txt - lines changed 116, context: html, text, full: html, text

7a0259e335a296b55b748ecc5e0a05196f29875d Fri Mar 3 10:51:16 2017 -0800

• catching up the primates refs #17545
  • src/hg/utils/phyloTrees/199way.nh - lines changed 1, context: html, text, full: html, text

0aa47108fc01ebc82c08dd355810308afa6a8041 Fri Mar 3 12:00:35 2017 -0800

• catching up with all mammals refs #17545
  • src/hg/utils/phyloTrees/209way.nh - lines changed 209, context: html, text, full: html, text

f4991091a1f033d3bb69e777b4a989a552cfa9ec Fri Mar 3 13:17:25 2017 -0800

• catching up with the primates and mammals refs #17545
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 196, context: html, text, full: html, text

3250e238380a526eef96db6efa7d948ae467b7c6 Fri Mar 3 14:17:45 2017 -0800

• catch up mammal and primate common names refs #17545
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 398, context: html, text, full: html, text

246124caaad43fc1cc1a402cdd7ff22603ceb8a6 Fri Mar 3 14:31:45 2017 -0800

• adding chainNet overrides for colAng1 refs #17545
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.chainNet.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/trackDb.ra - lines changed 2, context: html, text, full: html, text

2b3b58dab5475ebf604224eec335e3580cce73e8 Fri Mar 3 14:32:27 2017 -0800

• up to date with mammals and primates refs #17545
  • src/hg/utils/phyloTrees/209way.dissect.txt - lines changed 2919, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/209wayChainNet.pl - lines changed 219, context: html, text, full: html, text

3320e55d59f033e6af9d920c365bb51bda880c66 Fri Mar 3 14:52:08 2017 -0800

• chainNet for colAng1 and macNem1 refs #17545
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 147, context: html, text, full: html, text

db8181a3700622923e24fa8fe9eac8ccea739498 Fri Mar 3 15:03:42 2017 -0800

• adding chainNet overrides refs #18927
  • src/hg/makeDb/trackDb/macaca/macNem1/trackDb.chainNet.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macNem1/trackDb.ra - lines changed 2, context: html, text, full: html, text

ddb0eb195e5d5b4d53e6e55aef9cb4d2e61d03f8 Fri Mar 3 15:41:13 2017 -0800

• catching up names for primates and mammals refs #17545
  • src/hg/utils/phyloTrees/209way.commonNames.nh - lines changed 209, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/209way.scientificNames.nh - lines changed 209, context: html, text, full: html, text

d941d7db26da086ab15f4c2c3767744ca92b8737 Sat Mar 4 16:44:38 2017 -0800

• adding micMur3 Mouse lemur refs #18984
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text

4fa8a75ba2ed2551de9b4b962a45c1a8786a40a7 Mon Mar 6 09:37:57 2017 -0800

• adding rhiBie1 macNem1 micMur3 refs #18984 #18958 #18927
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 4, context: html, text, full: html, text

861d3471788fcc1fddbb6daa4e15a260a9016945 Mon Mar 6 09:43:52 2017 -0800

• adding rhiBie1 rules refs #18958
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

428279f27f702e6fcc17394a3b1dfa21d6920dca Mon Mar 6 10:23:05 2017 -0800

• v346 preview2 refs #18964
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text