Commits for hiram

v375_preview to v375_preview2 (2018-11-26 to 2018-12-03) v375

02a232e0d2292009a824295de5547f4f457c369d Mon Nov 26 10:18:39 2018 -0800

• adding cotJap2 chainNet lastz definitions refs #22330
  • src/hg/makeDb/trackDb/chicken/galGal6/chainNetBirds.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.birds.ra - lines changed 54, context: html, text, full: html, text

c28e944f96d346bd8b1f1895fad7fc77e77c884e Mon Nov 26 10:28:15 2018 -0800

• adding crispr 10K track refs #22330
  • src/hg/makeDb/trackDb/birds/cotJap2/trackDb.ra - lines changed 1, context: html, text, full: html, text

cc34104c13dd702c0ffe6a472cc0b01b6a428b87 Mon Nov 26 11:00:34 2018 -0800

• finish off cotJap2 lastz/chainNet and bosTau9 on hg38 refs #22330
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 165, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 8, context: html, text, full: html, text

157ae7b6fc196366a112335d1711301b55f8dd80 Mon Nov 26 11:19:01 2018 -0800

• QA Ready refs #22330
  • src/hg/makeDb/doc/cotJap2/initialBuild.txt - lines changed 365, context: html, text, full: html, text

5c099d22c8723ee83f05fe97d9897266960afa2e Tue Nov 27 09:59:30 2018 -0800

• better organization of the tree refs #18874
  • src/hg/htdocs/images/phylo/dm6_124way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

b939070d9eafdd9d916c86dd68748f94c14738f7 Tue Nov 27 10:18:31 2018 -0800

• completed 4d tree estimation refs #18874
  • src/hg/makeDb/doc/dm6/multiz124way.txt - lines changed 634, context: html, text, full: html, text

e564fce61a54e3611d8335ac9d7d4ed71dc89aa9 Tue Nov 27 11:15:16 2018 -0800

• visibility hide refs #18874
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayMafNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayRbest.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124waySyn.ra - lines changed 1, context: html, text, full: html, text

2c63b54a1f782f28122bab6cf7fc76f2edbad065 Wed Nov 28 09:47:12 2018 -0800

• print distance even when -noInternal refs #22113
  • src/hg/utils/phyloTrees/binaryTree.pl - lines changed 1, context: html, text, full: html, text

48b318233ab209b7a19ebe275f0cb3e068d77e62 Wed Nov 28 19:00:39 2018 -0800

• adding description page refs #18874
  • src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html - lines changed 1051, context: html, text, full: html, text

77ab001ecb4937b1a842a1089b521265651e81e0 Thu Nov 29 10:48:20 2018 -0800

• clarify target if fromDb and query is toDb refs #22546
  • src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 4, context: html, text, full: html, text

a04ef5a8563e40327e5885553ecd91b17ea56052 Thu Nov 29 11:41:59 2018 -0800

• proper ordering of tracks in the Comparative Genomics section refs #18874
  • src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.ra - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124way.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayMafNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124wayRbest.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124waySyn.ra - lines changed 1, context: html, text, full: html, text

5e97ba62ad1412cf711b5dd2370abd5ba2ba175c Fri Nov 30 10:20:28 2018 -0800

• change group flies to holometabola refs #22550
  • src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.ra - lines changed 1, context: html, text, full: html, text

93d216748e3e906fe0ac67ba7620c1c70fecfc82 Fri Nov 30 10:42:25 2018 -0800

• set specific ensGene outlink to their special grch37 site refs #22539
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text

36d8ba58967f7379a38ff3e6d78efa7152563dbe Fri Nov 30 11:13:37 2018 -0800

• set track labels to 124 insects instead of species refs #22550
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124way.ra - lines changed 4, context: html, text, full: html, text

612cccf76af0e88abd0fbe9e302e0afcc2138985 Fri Nov 30 12:59:28 2018 -0800

• eliminate the unnecessary subGroup2 clade selections refs #22550
  • src/hg/makeDb/trackDb/drosophila/dm6/trackDb.124way.ra - lines changed 6, context: html, text, full: html, text

32d4ec45f05fdc1b8634a225ac50c8724b6e41d5 Fri Nov 30 13:37:07 2018 -0800

• missing a closing semi colon ; on an nbsp tag no redmine
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 4, context: html, text, full: html, text

6c41a21bcb9ee787fda0ece49b20b02c8aec79d7 Fri Nov 30 13:41:14 2018 -0800

• adding html description page refs #22550
  • src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.html - lines changed 172, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/chainNetInsects.ra - lines changed 2, context: html, text, full: html, text

52717264a14fc9f930ec580215f1433069dede6c Fri Nov 30 13:44:44 2018 -0800

• QA ready refs #22550
  • src/hg/makeDb/doc/dm6/multiz124way.txt - lines changed 236, context: html, text, full: html, text

0d1eddfd96c689220bde25f45a534899fb9e8a79 Sun Dec 2 20:36:25 2018 -0800

• better organization for Drosophila refs #22550
  • src/hg/htdocs/images/phylo/dm6_124way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

7a6b5cb455c18a83028a3140c4e02bc3651f1c6f Mon Dec 3 10:16:10 2018 -0800

• v375 preview2, refs #22531
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text