Commits for hiram

v353_preview2 to v353_base (2017-07-31 to 2017-08-07) v353

57c6a4655f3ebb1b0be4632cd52c7b7a38430b8f Tue Aug 1 13:45:55 2017 -0700

• correct X1000 CFD scores and correct bug in splitGuidesEffScore.py refs #19874
  • src/hg/makeDb/crisprTrack/convOffs.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/crisprTrack/findGuides.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/crisprTrack/splitGuidesEffScore.py - lines changed 1, context: html, text, full: html, text

93ae6ca61e07b83a678f19e77f60801e5c6cefff Thu Aug 3 11:24:41 2017 -0700

• browser done per user request refs #19879 #19877
  • src/hg/makeDb/doc/oreNil3/initialBuild.txt - lines changed 74, context: html, text, full: html, text

ddff55a58b43e88492435c00b3da9445212673c0 Thu Aug 3 11:46:48 2017 -0700

• adding susScr11 rules refs #19859
  • src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text

bcee7a3e186f66738ac86859282f4b1ae252eb37 Thu Aug 3 13:33:50 2017 -0700

• tables test robot for preview2 week refs #19846
  • src/utils/qa/weeklybld/preview2TablesTestRobot.csh - lines changed 37, context: html, text, full: html, text

2ab056dc9cd0232722ec44cb7d824b6b8a67ecad Thu Aug 3 13:46:16 2017 -0700

• adding track viz overrides and defaults on refs #19879
  • src/hg/makeDb/trackDb/oreNil/oreNil3/trackDb.chainNet.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oreNil/oreNil3/trackDb.ra - lines changed 24, context: html, text, full: html, text

50b82c893180946bbb2a75cc511184e45300df12 Thu Aug 3 13:49:33 2017 -0700

• correct augustusGene override refs #19879
  • src/hg/makeDb/trackDb/oreNil/oreNil3/trackDb.ra - lines changed 1, context: html, text, full: html, text

a0fbb8a6c10c1cd79f2f6b7197affa529a7706bf Thu Aug 3 13:56:01 2017 -0700

• adding default viz and overrides refs #19859
  • src/hg/makeDb/trackDb/pig/susScr11/trackDb.chainNet.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra - lines changed 17, context: html, text, full: html, text

eb52ae40e4339827cc810992e44614b0cb3a6440 Thu Aug 3 14:05:36 2017 -0700

• finished browser refs #19859
  • src/hg/makeDb/doc/susScr11/initialBuild.txt - lines changed 91, context: html, text, full: html, text

432fcbc75dd12443681bd8dffead3980a6185ec9 Fri Aug 4 10:15:20 2017 -0700

• running up gorGor5 lastz chainNet to mm10 no redmine
  • src/hg/makeDb/doc/mm10.txt - lines changed 82, context: html, text, full: html, text

4885ef2c0d19f4082c45161a32a77d394861237c Fri Aug 4 10:21:38 2017 -0700

• completed oreNil3 and susScr11 browser builds refs #19859 #19879
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 141, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil2.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 16, context: html, text, full: html, text

83e451d52a5df644275bc7e6d983d97fcb791530 Fri Aug 4 10:22:56 2017 -0700

• add PATH to software/bin so the python scripts can find the python2.7 version refs #19514
  • src/hg/utils/automation/doCrispr.pl - lines changed 3, context: html, text, full: html, text

7a0758923f64f4fdc6b9e1ba16a8680c4adcbd43 Fri Aug 4 10:39:46 2017 -0700

• begin browser build for Regeneron refs #19937
  • src/hg/makeDb/doc/staAur1/initialBuild.txt - lines changed 619, context: html, text, full: html, text

564850e473874f9546797308e2c853db5f699a57 Fri Aug 4 10:45:18 2017 -0700

• Staphylococcus aureus from CDC public health image library refs #19937
  • src/hg/htdocs/images/Staphylococcus_aureus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

7bd130b6d7ffb1f1fe089ce8234ec3466be9549b Fri Aug 4 11:27:01 2017 -0700

• starting staAur1 browser for Regeneron refs #19937
  • src/hg/makeDb/trackDb/bacteria/staAur1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bacteria/staAur1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

4baa7c95b871d6a8094b24fe5fe10eab17316247 Fri Aug 4 14:18:55 2017 -0700

• adding staAur1 Staphylococcus aureus- refs #19937
  • 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

5d44320a592e3c6c72c9fa0410dd3c231e781007 Sat Aug 5 10:04:58 2017 -0700

• adding staAur1 to the update alignments refs #19337
  • 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

54b1ea018ead040c422fb22998fae1f44f48f3d6 Sat Aug 5 21:15:09 2017 -0700

• add rules for staAur1 assembly refs #19937
  • src/hg/makeDb/schema/all.joiner - lines changed 16, context: html, text, full: html, text

9feb1b6e1b4bedc62cc78a12770731dc56af7137 Sat Aug 5 21:50:34 2017 -0700

• adding Hep B virus, HPV, Staphylococcus aureus bacteria refs #19937
  • src/hg/js/dbDbTaxonomy.js - lines changed 28, context: html, text, full: html, text

1ae1dd4ba518cf8a4be15a5c58c37617bc526c3d Sun Aug 6 21:34:58 2017 -0700

• hgBbiDbLink should go out with userApps no redmine
  • src/hg/makeDb/makefile - lines changed 2, context: html, text, full: html, text

1beb3a09c1a3c93072908b2b6a4166d398ce3955 Mon Aug 7 09:49:30 2017 -0700

• v353 final build refs #19846
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

deb9aa671e2647557581e6c30265c1963ff45e2c Mon Aug 7 09:50:08 2017 -0700

• New version number v353
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text