Commits for hiram

v333_preview to v333_preview2 (2016-05-09 to 2016-05-16) v333

1e7484608fe7cd33713c45edc146656d3127d06c Mon May 9 12:51:03 2016 -0700

• done with 5-way alignment for galVar1 work refs #17180
  
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 552, context: html, text, full: html, text

6e836413b45adf79a0b6506f4d76c1821e1b688a Tue May 10 11:11:21 2016 -0700

• running up rn6 and danRer10 liftOver per user request refs #17015
  
  • src/hg/makeDb/doc/galGal5/lastzRuns.txt - lines changed 135, context: html, text, full: html, text

688c2522a9f59d2ebd1b90623af978034a36a9c4 Tue May 10 12:48:02 2016 -0700

• fixup build scripts to use USE_SAMTABIX and USE_HTS refs #17294
  
  • src/utils/qa/weeklybld/buildOneUseCase - lines changed 7, context: html, text, full: html, text
  • src/utils/qa/weeklybld/buildWithUseCases - lines changed 11, context: html, text, full: html, text

1ccf3ecaf1321b08f208b91beaadf92ec8151384 Tue May 10 13:17:59 2016 -0700

• fixup used uninitalized error refs #17294
  
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 1, context: html, text, full: html, text

e9710b55585be1902cfa409f78516550ac885fa5 Tue May 10 14:38:16 2016 -0700

• the USE_BAM=1 no longer works by itself refs #17294
  
  • src/utils/qa/weeklybld/buildWithUseCases - lines changed 2, context: html, text, full: html, text

9a5218072526a800793759c70f67b03139e6aac8 Tue May 10 15:00:20 2016 -0700

• adding 145way track from Michael Hiller refs #17286
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.145way.ra - lines changed 114, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

5501c4a87072310d0a1d3cb73789afe1e1763c13 Tue May 10 15:24:24 2016 -0700

• bringing in the new dbs to the lists in the sGroups refs #17286
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.145way.ra - lines changed 8, context: html, text, full: html, text

baeeba4fb0009f04327f01dd3b6368c8d627205c Wed May 11 12:44:33 2016 -0700

• done with downloads refs #17180
  
  • src/hg/makeDb/doc/galVar1/multiz5way.txt - lines changed 369, context: html, text, full: html, text

3cbae2bc1a4997e656bdc5a3f0588ebc009134cb Wed May 11 13:32:21 2016 -0700

• done with downloads refs #17180
  
  • src/hg/makeDb/doc/galVar1/lastzRuns.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/galVar1/multiz5way.txt - lines changed 2, context: html, text, full: html, text

96bf3436e5aa7b0cfe55bb44ebfad252f51c248e Wed May 11 14:20:04 2016 -0700

• indicate completion of augustusGenes refs #16744
  
  • src/hg/makeDb/doc/rheMac8/initialBuild.txt - lines changed 4, context: html, text, full: html, text

a3e9f9627a0222eb703f0e6605f86f749ca62877 Wed May 11 14:43:46 2016 -0700

• Added panPan2; refs #16036
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

bca454495f096c2eef65703c7d474dc2c9017b0d Thu May 12 11:25:51 2016 -0700

• adding danRer10 and rn6 chainNet tracks and overrides for galGal5 refs #17168
  
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.chainNet.ra - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 101, context: html, text, full: html, text

1639b63c7ebbb1033fa3643005081506b5371377 Thu May 12 14:26:57 2016 -0700

• expand list for ncbiRefSeq gene track assembly list refs #17180
  
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text

74616f6f2fb412c64d310a0a0bc592418a658e81 Thu May 12 16:01:24 2016 -0700

• verify required tables for minimal browser are present refs #17180
  
  • src/hg/utils/automation/makePushQSql.pl - lines changed 16, context: html, text, full: html, text

21c69a6ff98c7494cae3fc93f3e60b4570e99c74 Thu May 12 16:24:39 2016 -0700

• final bits for galGal5 refs #17168
  
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

472088b461aa19de0adbbb9bcc8f77a10d1139e2 Fri May 13 06:58:59 2016 -0700

• pelSin1 can get out of alpha status refs #17168
  
  • src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra - lines changed 1, context: html, text, full: html, text

17cf75ea7b36e3f53c319ed6de3bd4ae7c618622 Fri May 13 14:32:40 2016 -0700

• galGal5 now has ncbiRefSeq too refs #17168
  
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text

269ade0eca860da517c064fb6471a1bb72b26962 Fri May 13 14:43:13 2016 -0700

• run up liftOver to ce11 per user Kevin Howe request no redmine
  
  • src/hg/makeDb/doc/ce8.txt - lines changed 17, context: html, text, full: html, text

375b96b6a8e91ea7b3949a6bc4d739267939c3ee Fri May 13 14:43:55 2016 -0700

• clone ends done for rn6 refs #16100
  
  • src/hg/makeDb/doc/rn6.txt - lines changed 1, context: html, text, full: html, text

a56bfefdb7dab8ba5a3d4e2ff62cd21ff8110374 Fri May 13 14:50:02 2016 -0700

• galGal5 has the ucscToRefSeq track refs #17168
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ucscToRefSeq.html - lines changed 16, context: html, text, full: html, text

da98ad87161eefaf3d4bf83385c2eae856e2ec46 Fri May 13 15:15:27 2016 -0700

• done and in the pushQ refs #17168
  
  • src/hg/makeDb/doc/galGal5/initialBuild.txt - lines changed 112, context: html, text, full: html, text

cbc06c5f77761cd938db3b08adc13dc67658cabc Mon May 16 09:11:38 2016 -0700

• pelSin1 lastz/chain/net for galVar1 multiz refs #17180
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 72, context: html, text, full: html, text

866330207bfc065809be544929457db16c1a9ec9 Mon May 16 11:00:37 2016 -0700

• v333 preview2 refs #17202
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text