Commits for hiram

v356_preview to v356_preview2 (2017-09-25 to 2017-10-02) v356

f40c1fc25c5d19a45f4cbefa40d8b85607de84cd Mon Sep 25 10:30:07 2017 -0700

• Added neoSch1 Hawaiian monk seal/Neomonachus schauinslandi; refs #19883
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

414f4e39ab63c60f31bb1a72fef71f3e04c08938 Mon Sep 25 10:32:52 2017 -0700

• starting genbank run refs #19883
  • src/hg/makeDb/doc/neoSch1/initialBuild.txt - lines changed 112, context: html, text, full: html, text

256f810d40ff5409aa15fe93e7e78487fd4692d4 Mon Sep 25 10:55:30 2017 -0700

• add gold table search rule refs #20196
  • src/hg/makeDb/trackDb/primate/aotNan1/trackDb.ra - lines changed 5, context: html, text, full: html, text

2fc5d119c0abc92076ce63c71590940128fbcb81 Mon Sep 25 11:16:38 2017 -0700

• Added aotNan1 - Ma's night monkey - Aotus nancymaae refs #20196
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

8d35c4227fb1920dd8b1765db3bab3d3d95622c8 Mon Sep 25 11:18:47 2017 -0700

• starting genbank run refs #20196
  • src/hg/makeDb/doc/aotNan1/initialBuild.txt - lines changed 184, context: html, text, full: html, text

f91052636c9c8138b5fb5294bf047587a4a80225 Mon Sep 25 13:27:14 2017 -0700

• Added neoSch1 - Hawaiian monk seal - Neomonachus schauinslandi refs #19883
  • 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

dbb7e29cb7a8d6ef024c6e0572a4ff8f22030756 Tue Sep 26 08:42:21 2017 -0700

• Added manLeu1 - Drill/Mandrillus leucophaeus refs #20190
  • src/hg/makeDb/schema/all.joiner - lines changed 12, context: html, text, full: html, text

2bedcbdfd72537a7da852585942d1f0ef8296cbb Tue Sep 26 10:53:31 2017 -0700

• clean up browser bins list to make it neat no redmine
  • src/hg/makefile - lines changed 8, context: html, text, full: html, text

6752359ad20cca58f4f3745186716d5a2c70d549 Tue Sep 26 11:13:41 2017 -0700

• QA ready, done refs #20190
  • src/hg/makeDb/doc/manLeu1/initialBuild.txt - lines changed 134, context: html, text, full: html, text

73cd8f9f3fb103862b74fa29bc6467a5142442bf Tue Sep 26 15:11:19 2017 -0700

• adding phaCin1 koala, neoSch1 monk seal, odoTex1 white tailed deer no redmine
  • src/hg/utils/phyloTrees/216.nh - lines changed 216, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/216way.commonNames.nh - lines changed 216, context: html, text, full: html, text

ce6ba59953295ed47a5bc4fc64804b3b880367ae Wed Sep 27 08:30:37 2017 -0700

• Added cerAty1/Sooty mangabey; refs #20199
  • 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

6522d37d8dfe57ee9738511e5ba3b52aaa2727c9 Wed Sep 27 16:00:02 2017 -0700

• adding proCoq1 to the build refs #20235
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/proCoq1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/proCoq1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/proCoq1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/proCoq1/trackDb.ra - lines changed 8, context: html, text, full: html, text

bbee903d8c6a6068f499b67a806828c3a00438fa Wed Sep 27 17:08:53 2017 -0700

• adding cebCap1 to the build refs #20237
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/cebCap1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/cebCap1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/cebCap1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/cebCap1/trackDb.ra - lines changed 8, context: html, text, full: html, text

3c2a38ff7b34c9744f8c422719f4286f4238faa7 Wed Sep 27 17:11:55 2017 -0700

• running up repeatMasker refs #20237
  • src/hg/makeDb/doc/cebCap1/initialBuild.txt - lines changed 694, context: html, text, full: html, text

f95bb6ab09881baf877b9a931514cb27a8a77401 Wed Sep 27 17:12:37 2017 -0700

• running up repeatMasker refs #20235
  • src/hg/makeDb/doc/proCoq1/initialBuild.txt - lines changed 715, context: html, text, full: html, text

d5e6ed5eca12c09f8e4676f8c8c3331086a509ba Thu Sep 28 08:28:39 2017 -0700

• Added aotNan1 - Ma's night monkey - Aotus nancymaae refs #20196
  • 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

95185a22d3de451abfaa45a10cd03cf997f4f19c Thu Sep 28 10:55:15 2017 -0700

• ready for joinerCheck business refs #20196
  • src/hg/makeDb/doc/aotNan1/initialBuild.txt - lines changed 49, context: html, text, full: html, text

5183c67a0b661e16038bcb6a5e79c65efd1ab224 Thu Sep 28 10:59:53 2017 -0700

• adding rules for aotNan1 refs #20196
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

ca70de684794c992e9859ccefe8ff45d41757b2d Thu Sep 28 13:01:38 2017 -0700

• completed and in pushQ refs #20196
  • src/hg/makeDb/doc/aotNan1/initialBuild.txt - lines changed 14, context: html, text, full: html, text

210d1d9c7d0721e0034191a1739aef974b871689 Thu Sep 28 13:08:26 2017 -0700

• lastz chain net to manLeu1 aotNan1 neoSch1 cerAty1 refs #20196 #20199 #19883 #20190
  • src/hg/makeDb/doc/mm10.txt - lines changed 228, context: html, text, full: html, text

15379a1b22b23bc5101be9e4f2c93ec24b149b5b Thu Sep 28 13:46:53 2017 -0700

• Added proCoq1/Coquerel's sifaka; refs #20235
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

8c1c98849a35b8137b613298ee826026b074e988 Thu Sep 28 13:54:29 2017 -0700

• lastz runs for aotNan1 cerAty1 manLeu1 and neoSch1 refs #20196 #20199 #20190 #19883
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 279, context: html, text, full: html, text

c6d142cf98dce855c2664ac9a4588b34cbdbe8f8 Thu Sep 28 16:03:34 2017 -0700

• Added cebCap1/Cebus capucinus; refs #20237
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

2a685a33c9c3d58a9ae18f770d7548ce629b121b Thu Sep 28 17:10:20 2017 -0700

• Added proCoq1 - Coquerel's sifaka/Propithecus coquereli refs #20235
  • 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

01d5da01f26f7495eba206846795c65bb2b2fee9 Thu Sep 28 17:18:23 2017 -0700

• add gold/assembly track search rule refs #20235
  • src/hg/makeDb/trackDb/primate/proCoq1/trackDb.ra - lines changed 5, context: html, text, full: html, text

e0895be665ac16215e2272e354745eecd6d50e1e Thu Sep 28 17:29:36 2017 -0700

• Added cebCap1 - White-faced sapajou/Cebus capucinus imitator refs #20237
  • 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

c24669d5a126dd32e0b13a2f4de74208cea9957f Thu Sep 28 17:42:49 2017 -0700

• starting proCoq1 and cerCap1 lastz runs refs #20235 #20237
  • src/hg/makeDb/doc/mm10.txt - lines changed 114, context: html, text, full: html, text

a125ca30634b3ace6e690af42319c69e6b081a71 Fri Sep 29 10:17:48 2017 -0700

• adding rules for cerAty1 refs #20199
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

06e948d48841886e21bfabad9e06dd2ef73fb5d6 Fri Sep 29 14:27:10 2017 -0700

• completed and in the pushQ refs #20199
  • src/hg/makeDb/doc/cerAty1/initialBuild.txt - lines changed 51, context: html, text, full: html, text

933cff97fa09822f8ebe7c52eff56ddd307cb21e Mon Oct 2 10:24:40 2017 -0700

• v356 preview2 refs #20233
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text