Commits for hiram

v358_preview to v358_preview2 (2017-11-06 to 2017-11-13) v358

0bad03b9bf82a3bdc76ad385fca8cc3944feac7f Mon Nov 6 18:55:19 2017 -0800

• ready for final README business refs #20216
  • src/hg/makeDb/doc/hg38/multiz30way.txt - lines changed 719, context: html, text, full: html, text

24db880787d590d5498eaeb0ff8a48b9a0ca26d0 Tue Nov 7 14:31:49 2017 -0800

• marked QA Ready in redmine refs #20216
  • src/hg/makeDb/doc/hg38/multiz30way.txt - lines changed 49, context: html, text, full: html, text

6f2548f27be2cb58f3182f666247187915966fbd Wed Nov 8 11:02:24 2017 -0800

• correct case Primates on short/long labels refs #20216
  • src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra - lines changed 2, context: html, text, full: html, text

55307ac92fbd30177b01d37d223762b6a23a52d5 Wed Nov 8 14:05:55 2017 -0800

• indicate in the option help message about the load option refs #20216
  • src/hg/utils/automation/doRecipBest.pl - lines changed 1, context: html, text, full: html, text

d267cc65008bc191852edb2ef1cbd10909c7bf4c Wed Nov 8 16:55:24 2017 -0800

• updating entries for pseHum cheMyd apaSpi pelSin chrPic xipMac lepOcu astMex neoBri hapBur mayZeb punNye oreNil takFla refs #20216
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 52, context: html, text, full: html, text

5ad9b79049b68350df23ceacaf4b470315125ed2 Wed Nov 8 18:44:44 2017 -0800

• all definitions RR, Dev, old, new in one file refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 1609, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 374, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestPrimate.ra - lines changed 450, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSynPrimate.ra - lines changed 450, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 871, context: html, text, full: html, text

ee48295c6a2004c7565638e79dfca2d7780dadf8 Wed Nov 8 18:46:33 2017 -0800

• all definitions RR, Dev, old, new in one file refs #20216
  • src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 6, context: html, text, full: html, text

b028072ddb1514f01b1a344c82f0301ad7f2f863 Wed Nov 8 18:47:13 2017 -0800

• all definitions RR, Dev, old, new in one file refs #20216
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 5, context: html, text, full: html, text

483bd226bd99ba10c031dc94bfd7836906214bb6 Wed Nov 8 19:01:57 2017 -0800

• do not need gorGor1 or the older RBest definitions refs #20216
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 118, context: html, text, full: html, text

7fb26d0f921500423931f0633d54db3c0d872827 Wed Nov 8 19:24:57 2017 -0800

• correct comment label on gorGor4 entry refs #20216
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 1, context: html, text, full: html, text

093e780f33158478d0fcd2dc655c836811f82b34 Wed Nov 8 21:03:17 2017 -0800

• add listings for use with constructing Primates Placentals and Vertebrates chainNet composites refs #20216
  • src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/afrotheria.list - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/amphibia.list - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/carnivora.list - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/cercopithecinae.list - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/cetartiodactyla.list - lines changed 29, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/chiroptera.list - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/coelancanthimorpha.list - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/cryptodira.list - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/dinosauria.list - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/euarchontoglires.list - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/haplorrhini.list - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/hominidae.list - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/hyperoartia.list - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/laurasiatheria.list - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/lepidosauria.list - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/makefile - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/mammalia.list - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/neopterygii.list - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/perissodactyla.list - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/strepsirrhini.list - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/chainNetComposites/xenarthra.list - lines changed 4, context: html, text, full: html, text

15bcb203326a8118ac315da58157c63f6123c978 Mon Nov 13 09:47:46 2017 -0800

• v358 preview2 refs #20479
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text