Commits for hiram

v334_preview to v334_preview2 (2016-05-31 to 2016-06-06) v334

49feb41a341d3ae6f20c18a744e6dfee86d8ae22 Tue May 31 13:56:53 2016 -0700

• photo from Robert Pitman NOAA https://upload.wikimedia.org/wikipedia/commons/3/37/Killerwhales_jumping.jpg refs #17425
  
  • src/hg/htdocs/images/Orcinus_orca.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

3db1bd39e85a02a999d436459703f0fe8d99add7 Tue May 31 15:17:22 2016 -0700

• allow ncbiBioSample variable in the config.ra file refs #17425
  
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 7, context: html, text, full: html, text

8f6a6c2148e3523e9c9159355b0c59d5e6a223e7 Tue May 31 15:58:33 2016 -0700

• adding orcOrc1 to the build refs #17425
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/trackDb.ra - lines changed 8, context: html, text, full: html, text

3e4c7799848278c6c3d10c85ef6b5dcc486d66a4 Tue May 31 16:09:56 2016 -0700

• initial build for orcOrc1 underway refs #17425
  
  • src/hg/makeDb/doc/orcOrc1/initialBuild.txt - lines changed 636, context: html, text, full: html, text

b4064bac1906917d049c19ac0734e3246e5daff8 Wed Jun 1 11:31:44 2016 -0700

• Added orcOrc - Orcinus orca (killer whale) refs #17425
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text

786076aa72e112e87ca704002fd9548033511d08 Wed Jun 1 15:43:01 2016 -0700

• adding rules for orcOrc1 refs #17425
  
  • src/hg/makeDb/schema/all.joiner - lines changed 11, context: html, text, full: html, text

c01c5bbd37ac611d306b36c2754d1927ea6986dd Thu Jun 2 13:07:21 2016 -0700

• adding orcOrc1 chain net refs #17425
  
  • src/hg/makeDb/trackDb/cow/bosTau8/trackDb.chainNet.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau8/trackDb.ra - lines changed 1, context: html, text, full: html, text

0e7a9b03acb884c21c65228faec2efe6df6eaf11 Thu Jun 2 13:10:56 2016 -0700

• Added orcOrc1 - killer whale - Orcinus orca - refs #17425
  
  • 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

f92e2279b961c6c264c0efeef674583a40f8171f Thu Jun 2 13:46:49 2016 -0700

• adding search rule for gold/assembly track refs #17425
  
  • src/hg/makeDb/trackDb/whale/orcOrc1/trackDb.ra - lines changed 5, context: html, text, full: html, text

8b91241691f366e826cf701fd58e485aa09e094a Thu Jun 2 13:47:47 2016 -0700

• just about ready for pushQ entry refs #17425
  
  • src/hg/makeDb/doc/orcOrc1/initialBuild.txt - lines changed 124, context: html, text, full: html, text

cbd881859024572ff079cb0890b07fe7accdc49c Fri Jun 3 09:58:05 2016 -0700

• fixup release tags to avoid errors in tdbQuery refs #17425
  
  • src/hg/makeDb/trackDb/cow/bosTau8/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text

ba24048d3f5ab41c8f8ad127ac67b908535c8097 Fri Jun 3 10:07:00 2016 -0700

• lastz chain net to orcOrc1 per user request refs #17425
  
  • src/hg/makeDb/doc/bosTau8.txt - lines changed 56, context: html, text, full: html, text

1cdb96fce1eadd6476ebf2dfbe11642c5ec9042c Fri Jun 3 10:27:05 2016 -0700

• allow ncbiBioSample in the config.ra file refs #17425
  
  • src/hg/utils/automation/makeDownloads.pl - lines changed 4, context: html, text, full: html, text

1d50150f86e036e6573adc2489cb423e9d916d1e Fri Jun 3 13:22:26 2016 -0700

• catching up on previous lastz runs refs #17425
  
  • src/hg/makeDb/doc/orcOrc1/lastzRuns.txt - lines changed 129, context: html, text, full: html, text

0f071c122e550f72b077b13dd0e891d9c4159235 Fri Jun 3 14:56:26 2016 -0700

• add comparison track for refGene to ncbiRefSeq refs #13673
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 37, context: html, text, full: html, text

168d1ae1702ea8b5da03e31531dcf47379a82e57 Mon Jun 6 10:16:11 2016 -0700

• v334 preview2 refs #17457
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text