Commits for hiram

v298_preview2 to v298_base (2014-03-31 to 2014-04-07) v298

• done with masking refs #12977
  • src/hg/makeDb/doc/balAcu1.txt - lines changed 68, context: html, text, full: html, text
• adding balAcu1 Minke whale refs #12977
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• adding definition for balAcuNames refs 12977
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding definition for balAcuNames refs 12977
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
• Elephant shark photo from http://www.flagstaffotos.com.au/ Wikipedia refs #12976
  • src/hg/htdocs/images/Callorhinchus_milii.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• initial files from makeGenomeDb.pl refs #12976
  • src/hg/makeDb/trackDb/calMil/calMil1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding calMil1 to the build refs #12976
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial sequence and running masking refs #12976
  • src/hg/makeDb/doc/calMil1.txt - lines changed 347, context: html, text, full: html, text
• adding calMil1 Elephant shark refs #12976
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding balAcu1 and calMil1 Minke whale and Elephant shark refs #12976 #12977
  • src/hg/makeDb/schema/all.joiner - lines changed 12, context: html, text, full: html, text
• Chinese hamster photo from WikiMedia commons refs #6506
  • src/hg/htdocs/images/Cricetulus_griseus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Added balAcu1 to daily hgwdev build refs #12977
  • 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
• start monDom5 swap refs #8212
  • src/hg/makeDb/doc/rn5.txt - lines changed 6, context: html, text, full: html, text
• syntenic net for hg38 for 14-way refs #8212
  • src/hg/makeDb/doc/rn5.txt - lines changed 4, context: html, text, full: html, text
• temporarily set cons60way to hide while maf table is reloaded refs #12260
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 1, context: html, text, full: html, text
• recip best for Panda for 13-way alignment refs #8212
  • src/hg/makeDb/doc/rn5.txt - lines changed 1, context: html, text, full: html, text
• connection to hgwbeta for commands requires extra business now refs #12977
  • src/hg/utils/automation/makePushQSql.pl - lines changed 2, context: html, text, full: html, text
• no mapviewer for hg18 and hg19 now uses build=previous and add hg38 link to NCBI refs #12871
  • src/hg/hgTracks/menu.c - lines changed 3, context: html, text, full: html, text
• initial files from makeGenomeDb.pl refs #6506
  • src/hg/makeDb/trackDb/criGri/criGri1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGri1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGri1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding criGri1 to the build refs #6506
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• Added calMil1 to daily hgwdev build refs #12976
  • 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
• genbank done constructing download files refs #12976
  • src/hg/makeDb/doc/calMil1.txt - lines changed 147, context: html, text, full: html, text
• fixup ensGene name display from code review refs #12957
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
• mysql create table now requires ENGINE and not TYPE refs #12976
  • src/hg/utils/automation/makePushQSql.pl - lines changed 1, context: html, text, full: html, text
• moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
  • src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cpgIslandSuper.html - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 28, context: html, text, full: html, text
• change the discussion of masked and unmasked versions to eliminate the hg38 specific language refs #12976 #12977
  • src/hg/makeDb/trackDb/cpgIslandSuper.html - lines changed 7, context: html, text, full: html, text
• in the pushQ refs #12976
  • src/hg/makeDb/doc/calMil1.txt - lines changed 8, context: html, text, full: html, text
• set default track visibilities refs #12976
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• setting default track visibilities refs #12977
  • src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra - lines changed 7, context: html, text, full: html, text
• fix gap procedure steps refs #12976
  • src/hg/makeDb/doc/calMil1.txt - lines changed 4, context: html, text, full: html, text
• in the pushQ refs #12977
  • src/hg/makeDb/doc/balAcu1.txt - lines changed 210, context: html, text, full: html, text
• v298 final build refs #12803
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v298
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text