Commits for hiram

v346_preview2 to v346_base (2017-03-06 to 2017-03-13) v346

80f1efa46072b85dfefc166be32c496ad3c59e1c Mon Mar 6 10:27:22 2017 -0800

• adding micMur3 rules refs #18984
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text

69ae6eae872158f15257f905a0273f291ff2eefe Mon Mar 6 10:48:12 2017 -0800

• in pushQ 008055 refs #18927
  • src/hg/makeDb/doc/macNem1/initialBuild.txt - lines changed 240, context: html, text, full: html, text

4db8a7e372080ca18102149cba402ffdc0f3ce7b Mon Mar 6 10:52:27 2017 -0800

• in pushQ 008056 refs #18958
  • src/hg/makeDb/doc/rhiBie1/initialBuild.txt - lines changed 22, context: html, text, full: html, text

05a4f0aef0d087b201bb37fc85357e1e745f1ce3 Mon Mar 6 13:17:10 2017 -0800

• up to date with new assemblies colAng1 rhiBie1 macNem1 updated taxId for tarSyr2 caeSp51
  • src/hg/js/dbDbTaxonomy.js - lines changed 58, context: html, text, full: html, text

857f1ea75e920cb0a125aca645cd0002918b848b Mon Mar 6 13:35:43 2017 -0800

• updated instructions to eliminate more non-UCSC db names from output refs #17545
  • src/hg/makeDb/doc/dbDbTaxonomy.txt - lines changed 10, context: html, text, full: html, text

103ead3ed5a7f529071fce0a59e4ba3200fd76e4 Mon Mar 6 14:38:23 2017 -0800

• in pushQ 008057 refs #18984
  • src/hg/makeDb/doc/micMur3/initialBuild.txt - lines changed 198, context: html, text, full: html, text

877ccdf3659e0021265facea567fd261a546d3cd Mon Mar 6 14:39:02 2017 -0800

• adding micMur3 lastz/chain/net refs #18984
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 70, context: html, text, full: html, text

bbd3543c7801028cb11f2f9c8793e93c4221e0c6 Tue Mar 7 13:24:30 2017 -0800

• added blat server and set default position refs #18984
  • src/hg/makeDb/doc/micMur3/initialBuild.txt - lines changed 7, context: html, text, full: html, text

6c404ee8560fdc4bdba31829dba5fd7c2bf58e0e Wed Mar 8 10:03:33 2017 -0800

• completed lastz/chain/net for mm10 vs micMur3 refs #18984
  • src/hg/makeDb/doc/micMur3/initialBuild.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 64, context: html, text, full: html, text

458f66d844ac66ef254d0700852c1af7c7fcd9c8 Wed Mar 8 14:29:59 2017 -0800

• adding tupChi1 to the build refs #10146
  • src/hg/makeDb/trackDb/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra - lines changed 8, context: html, text, full: html, text

6d623c6ae1ddad24db445814fa8caf536696d325 Wed Mar 8 14:41:43 2017 -0800

• add gold search rule refs @10146
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/trackDb.ra - lines changed 5, context: html, text, full: html, text

f9f77886f3b4986248ec97ff059bd8031c9f65d3 Wed Mar 8 15:28:37 2017 -0800

• allow names other than ^chr to work for chain filter by name refs #18656
  • src/hg/hgTracks/chainTrack.c - lines changed 4, context: html, text, full: html, text

cf12124242c9a27a19376237b94e6bf7ff50126b Wed Mar 8 15:31:52 2017 -0800

• catching up build procedure on this old assembly refs #10146
  • src/hg/makeDb/doc/tupChi1/initialBuild.txt - lines changed 706, context: html, text, full: html, text

0388a9a6ff3443209d1e42c7afdea9169b266f89 Wed Mar 8 21:30:28 2017 -0800

• Added tupChi1; refs #10146
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

b1eb9e768e43105c374302cf62800fbfe8d65a5e Thu Mar 9 11:16:30 2017 -0800

• empty string is the same as All refs #18656
  • src/hg/hgTracks/chainTrack.c - lines changed 1, context: html, text, full: html, text

49b5f3eb273c28ef325f724a1ce843f019f749b3 Thu Mar 9 13:18:35 2017 -0800

• fix ooc reference for tupChi1 refs #10146
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text

ad71caddcd1a4f81b9630ef6c3fb2c703408b2bd Thu Mar 9 18:31:24 2017 -0800

• adding tupChi1 to the update alignments refs #10146
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text

6abfcff2881a216558f938357eceb8f4403fd979 Fri Mar 10 10:45:49 2017 -0800

• add ensGene construction procedure refs #19038
  • src/hg/makeDb/doc/chlSab2/initialBuild.txt - lines changed 42, context: html, text, full: html, text

22fac64197187f4a15144117a8f51385c9a17a8f Fri Mar 10 13:41:38 2017 -0800

• adding tupChi1 rules refs #10146
  • src/hg/makeDb/schema/all.joiner - lines changed 17, context: html, text, full: html, text

c0281656f631972d16a5ad9ff2ded246a6935dc5 Fri Mar 10 13:49:32 2017 -0800

• adding chlSab2 to ensGene rules refs #19038
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text

d35c7a1fdef8b47fe153d7f2fbbc43229f4f961a Mon Mar 13 09:58:28 2017 -0700

• v346 final build refs #18964
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

8a6afbbee7c7de66122e80b34daec9244819c4c7 Mon Mar 13 09:59:08 2017 -0700

• New version number v346
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text