Commits for hiram

v356_preview2 to v356_base (2017-10-02 to 2017-10-09) v356

466229ba187359d68a2c8c3047da4a3705f1bba7 Mon Oct 2 14:07:07 2017 -0700

• correctly escape organism common name that my have single quote marks refs #20265
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 6, context: html, text, full: html, text

845bd7c6663afa7a97050c97d21ddaee40b1b946 Mon Oct 2 14:10:40 2017 -0700

• photo from David Haring/Duke Lemur Center refs #20265
  • src/hg/htdocs/images/Eulemur_flavifrons,jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

6618ddc09ac5153aeabba20bd38c7088e88ba3da Mon Oct 2 14:18:16 2017 -0700

• photo from David Haring/Duke Lemur Center refs #20265
  • src/hg/htdocs/images/Eulemur_flavifrons.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

fd5f9c04e20970a124db1d103185c988a9ded98a Mon Oct 2 14:22:33 2017 -0700

• adding eulFal1 to the browser refs #20265
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulFla1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulFla1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulFla1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulFla1/trackDb.ra - lines changed 8, context: html, text, full: html, text

3027fa667b573f3b541458ae6e5c1aebae19a88c Mon Oct 2 14:28:20 2017 -0700

• correct reference to David Haring/Duke Primate Center for the photograph refs #20265
  • src/hg/makeDb/trackDb/primate/eulFla1/description.html - lines changed 2, context: html, text, full: html, text

8004fa20b262bb782228261a6370a6623d9eeca2 Mon Oct 2 14:32:31 2017 -0700

• running up repeatMasker refs #20265
  • src/hg/makeDb/doc/eulFla1/initialBuild.txt - lines changed 755, context: html, text, full: html, text

8718acc2eff6cede487bbbdf3117c897700d0591 Mon Oct 2 14:47:55 2017 -0700

• photo from David Haring/Duke Lemur Center refs #20266
  • src/hg/htdocs/images/Eulemur_macaco.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

d6dad1d758703e6d95d8b48773dd6233ff5c052d Tue Oct 3 13:07:17 2017 -0700

• finish off lastz chainNet runs for cerAty1 proCoq1 cebCap1 refs #20199 #20235 #20237
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 139, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 18, context: html, text, full: html, text

85e602552695078b2003350fb23235049c2797e9 Tue Oct 3 13:32:14 2017 -0700

• adding proCoq1 rules refs #20235
  • src/hg/makeDb/schema/all.joiner - lines changed 11, context: html, text, full: html, text

19736a52d7a9faa57f2f4aa6de3cf0f6d29d346b Tue Oct 3 14:27:39 2017 -0700

• adding gold assembly table search rule refs #20265
  • src/hg/makeDb/trackDb/primate/eulFla1/trackDb.ra - lines changed 5, context: html, text, full: html, text

2144cef3d22ded907c6430ac1eef40bce59576c8 Tue Oct 3 14:55:36 2017 -0700

• adding eulFla1 and eulMac1 refs #20265 #20266
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 4, context: html, text, full: html, text

dac22096644161f9f3fc43e447726b17fddaa652 Tue Oct 3 14:59:25 2017 -0700

• running genbank and lastz hg38 mm10 refs #20265
  • src/hg/makeDb/doc/eulFla1/initialBuild.txt - lines changed 148, context: html, text, full: html, text

ae23939b0f3b5b9bb953a7feac45b29dc1f4d52a Tue Oct 3 15:15:29 2017 -0700

• adding eulMac1 to the browser refs #20266
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulMac1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulMac1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulMac1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/primate/eulMac1/trackDb.ra - lines changed 8, context: html, text, full: html, text

f02549bd0ec06ce5ff5d4da0a1261bbf04c0962a Wed Oct 4 15:49:13 2017 -0700

• Added eulFla1 - Sclater's lemur - Eulemur flavifrons refs #20265
  • 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

68ebe6fd2404b559a4eef5794784e56c3970aac6 Wed Oct 4 15:56:14 2017 -0700

• running up cebCap1 and eulMac1 lastz/chainNet refs #20237 #20265
  • src/hg/makeDb/doc/mm10.txt - lines changed 114, context: html, text, full: html, text

beb04dc638d72f491110d6ef62e5de61b170c6bf Wed Oct 4 20:59:41 2017 -0700

• adding gold assembly track search rule refs #20266
  • src/hg/makeDb/trackDb/primate/eulMac1/trackDb.ra - lines changed 5, context: html, text, full: html, text

2dabf9bf784322465f55f3b457236a1a7170af75 Wed Oct 4 21:14:29 2017 -0700

• Added eulMac1 - Black lemur - Eulemur macaco refs #20266
  • 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

f95cc28fb6c730509dc38a2b1d28ff5d455a1232 Thu Oct 5 08:49:01 2017 -0700

• correct GCA identifier refs #17580
  • src/hg/makeDb/trackDb/gorilla/gorGor5/description.html - lines changed 1, context: html, text, full: html, text

0279b1f1a884ea9271a62592dbbd4c580fa3513b Thu Oct 5 11:37:01 2017 -0700

• completed, in the pushQ refs #20235
  • src/hg/makeDb/doc/proCoq1/initialBuild.txt - lines changed 170, context: html, text, full: html, text

fb84b31e56fb500e71a9622d9756e75f7184f13e Fri Oct 6 08:11:12 2017 -0700

• adding rules for eulFla1 and eulMac1 refs #20265 #20266
  • src/hg/makeDb/schema/all.joiner - lines changed 12, context: html, text, full: html, text

0bc02574b0f890fd2e1a1dead2e84b4eaba123c4 Fri Oct 6 08:21:59 2017 -0700

• completed lastz/chainNet runs for cebCap1, eulFla1, eulMac1 refs #20265 #20266 #20237
  • src/hg/makeDb/doc/mm10.txt - lines changed 65, context: html, text, full: html, text

ad55d247b89abf49a41959a7afa9e393c8afa4a2 Fri Oct 6 08:22:34 2017 -0700

• completed lastz/chainNet runs for eulFla1 and eulMac1 refs #20265 #20266
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 138, context: html, text, full: html, text

27b7db1cb0d4b9f16270a7d3bf7f0eed6f6ddc0f Fri Oct 6 13:05:49 2017 -0700

• completed and in pushQ refs #20265
  • src/hg/makeDb/doc/eulFla1/initialBuild.txt - lines changed 74, context: html, text, full: html, text

6ff3a348c93096e43256b2464f44a233849e1fca Fri Oct 6 13:09:49 2017 -0700

• complete and in pushQ refs #20266
  • src/hg/makeDb/doc/eulMac1/initialBuild.txt - lines changed 708, context: html, text, full: html, text

93fabb375cf33bd956ebae16abf80200ccdb9b5c Fri Oct 6 13:24:47 2017 -0700

• adding cerAty1 manLeu1 aotNan1 cebCap1 micMur1 proCoq1 eulMac1 eulFla1 lepWed1 neoSch1 refs #20190 #20196 #20237 #18984 #20235 #20266 #20265 #19883
  • src/hg/js/dbDbTaxonomy.js - lines changed 24, context: html, text, full: html, text

34695ee6ca36f4c18fc24392bce919548618b322 Mon Oct 9 09:59:18 2017 -0700

• v356 final build refs ##20233
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

8248a721c03198c87194c2c684685d395df82847 Mon Oct 9 10:00:06 2017 -0700

• New version number v356
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text