Commits for hiram

v375_base to v376_preview (2018-12-10 to 2018-12-17) v376

3cd24da966ff1bd7b2056dc22d8e49546b85a554 Mon Dec 10 10:07:07 2018 -0800

• phylo tree for ce11 135-way refs #22599
  • src/hg/htdocs/images/phylo/ce11_135way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

8a1174e0a3b81f1538d200c80b8c2d50b90c0aeb Mon Dec 10 14:09:12 2018 -0800

• done through iRow annotation refs #22599
  • src/hg/makeDb/doc/ce11/multiz135way.txt - lines changed 2623, context: html, text, full: html, text

16e228a41bf8b7506cee7a2fa155a54a6c17db9b Thu Dec 13 14:43:03 2018 -0800

• initial files from makeGenomeDb.pl refs #19937
  • src/hg/makeDb/trackDb/bacteria/staAur2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur2/gap.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur2/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra - lines changed 8, context: html, text, full: html, text

25d438880923505ec11c1a8ea5f3b67293a1f21b Thu Dec 13 14:50:53 2018 -0800

• add gold/assembly search rule refs #19937
  • src/hg/makeDb/trackDb/bacteria/staAur2/trackDb.ra - lines changed 6, context: html, text, full: html, text

831c1e4a0ef39cfa4b16bd712558821797e0ef70 Fri Dec 14 11:36:34 2018 -0800

• now working with database lists that may not actually be databases refs #18874
  • src/hg/utils/phyloTrees/chainNetCompositeTrackDb.pl - lines changed 50, context: html, text, full: html, text

d74188df6210bb2cf73bfb6bff3af47ee5b2bfa5 Fri Dec 14 12:41:05 2018 -0800

• composite track for all chain net tracks refs #22599
  • src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.ra - lines changed 1330, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 2, context: html, text, full: html, text

fcdd3425e1062d3808a1ccf85e24609591460b38 Fri Dec 14 12:46:05 2018 -0800

• remove the .ordered from the labels refs #22599
  • src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.ra - lines changed 1, context: html, text, full: html, text

5bc6c34e4bcaaafc8a5113734658659ad3af88eb Fri Dec 14 12:53:52 2018 -0800

• adding html page for this composite refs #22599
  • src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.html - lines changed 172, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/chainNetNematodes.ra - lines changed 1, context: html, text, full: html, text

51506aea54e26f8a2837e35f91b4656b6d8601fd Fri Dec 14 13:40:52 2018 -0800

• first look at 135-way multiz refs #22599
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra - lines changed 113, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.ra - lines changed 1, context: html, text, full: html, text

43cd1b612fb01fc85888df9c16a618a1b725699a Fri Dec 14 15:49:03 2018 -0800

• running phyloP refs #22599
  • src/hg/makeDb/doc/ce11/multiz135way.txt - lines changed 476, context: html, text, full: html, text

c4bc784cebbf4074de507ec3bf32154bcaedafc6 Sat Dec 15 16:07:23 2018 -0800

• record the 4d distance adjusted phylo trees refs #22599
  • src/hg/makeDb/doc/ce11/ce11.135way.scientificName.nh - lines changed 135, context: html, text, full: html, text
  • src/hg/makeDb/doc/ce11/ce11.135way.sequenceName.nh - lines changed 135, context: html, text, full: html, text
  • src/hg/makeDb/doc/ce11/ce11.135way.taxId.nh - lines changed 135, context: html, text, full: html, text

192feaea8c95a262f46aad739936cdb4da1e012e Sat Dec 15 16:24:35 2018 -0800

• add the taxonomy procedures and finishing up with download construction refs #22599
  • src/hg/makeDb/doc/ce11/multiz135way.txt - lines changed 162, context: html, text, full: html, text

544ac417e26ac22f657752566cea925f54f70a2b Sat Dec 15 17:26:06 2018 -0800

• now correctly 119 nematodes, flatworms and ci3 with description page table refs #22599
  • src/hg/makeDb/trackDb/worm/ce11/cons135way.html - lines changed 1106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/trackDb.135way.ra - lines changed 9, context: html, text, full: html, text

b6898620988fedd37c5f627c4570002d2580c2f8 Sat Dec 15 17:28:49 2018 -0800

• adding the sGroups for the ce11 135-way refs #22599
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 8, context: html, text, full: html, text

ccb8cb2787ef3ff16d882267f11b27f726278798 Mon Dec 17 09:56:10 2018 -0800

• v376 preview1, refs #22531
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text