Commits for hiram

v312_preview2 to v312_base (2015-02-09 to 2015-02-16) v312

• tarSyr2 doesn't have any native ESTs don't bother with them refs #14820
  
  • src/hg/makeDb/doc/tarSyr2/initialBuild.txt - lines changed 1, context: html, text, full: html, text
• done with lastz alignments for anoCar2 cheMyd1 chrPic2 xipMac1 punNye1 mayZeb1 danRer10 petMar2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 368, context: html, text, full: html, text
• fix left label offset difficulty refs #9741
  
  • src/hg/hgTracks/rmskJoinedTrack.c - lines changed 2, context: html, text, full: html, text
• lastz alignment to panTro4 per user request refs #14793
  
  • src/hg/makeDb/doc/calJac3.txt - lines changed 73, context: html, text, full: html, text
• lastz alignment to panTro4 per user request refs #14793
  
  • src/hg/makeDb/doc/panTro4.txt - lines changed 23, context: html, text, full: html, text
• forgot to load the phastCons track refs #14410
  
  • src/hg/makeDb/doc/tarSyr2/multiz17way.txt - lines changed 17, context: html, text, full: html, text
• fixup default visibility refs #9741
  
  • src/hg/makeDb/trackDb/joinedRmskComposite.ra - lines changed 1, context: html, text, full: html, text
• done with oryAfe1 cerSim1 chrAsi1 eptFus1 tupChi1 equCab2 camFer1 vicPac2 turTru2 orcOrc1 speTri2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 849, context: html, text, full: html, text
• done with cerSim1 chrAsi1 tupChi1 camFer1 turTru2 orcOrc1 speTri2 and starting runs for pteAle1 susScr3 loxAfr3 hetGla2 pteVam1 felCat8 ailMel1 musFur1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 myoDav1 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 1408, context: html, text, full: html, text
• correct assembly date is July 2007 refs #14835
  
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html - lines changed 1, context: html, text, full: html, text
• wrapping up pteAle1 loxAfr3 hetGla2 pteVam1 felCat8 ailMel1 musFur1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 myoDav1 camFer1 vicPac2 equCab2 and starting capHir1 myoLuc2 eleEdw1 triMan1 jacJac1 chiLan1 conCri1 octDeg1 ochPri3 eriEur2 echTel2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 1155, context: html, text, full: html, text
• Ensembl link could be elsewhere, allow trackDb override default refs #14462
  
  • src/hg/hgc/hgc.c - lines changed 3, context: html, text, full: html, text
• add faAlign to the utils list since it is used in the Ebola construction refs #14278
  
  • src/utils/makefile - lines changed 2, context: html, text, full: html, text
• adding checkUmask.sh to the userApps build fetch refs #14507
  
  • src/userApps/fetchKentSource.sh - lines changed 1, context: html, text, full: html, text
• remove redundent o_db in the net description refs #14410
  
  • src/hg/makeDb/trackDb/chainNet.html - lines changed 1, context: html, text, full: html, text
• adding description and placed track in compGeno refs #14278
  
  • src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra - lines changed 1, context: html, text, full: html, text
• adding description and placed track in compGeno refs #14278
  
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra - lines changed 1, context: html, text, full: html, text
• copleted loxAfr3 hetGla2 pteVam1 cavPor3 dasNov3 oryCun2 panHod1 lepWed1 odoRosDiv1 continuing pteAle1 susScr3 felCat8 ailMel1 musFur1 myoDav1 capHir1 myoLuc2 eleEdw1 jacJac1 chiLan1 conCri1 octDeg1 ochPri3 eriEur2 echTel2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 177, context: html, text, full: html, text
• starting rn6 criGri1 mesAur1 micOch1 sorAra2 macEug2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 462, context: html, text, full: html, text
• temporarily add donnak to final build report emails to cover Ann outage next week refs #14821buildEnv.csh
  
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 4, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doNewReview2.csh - lines changed 1, context: html, text, full: html, text
• temporarily add donnak to final build report emails to cover Ann outage next week refs #14821
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 1, context: html, text, full: html, text
• completed pteAle1 susScr3 felCat8 ailMel1 micFur1 myoDav1 chiLan1 octDeg1 eriEur2 echTel2 starting capHir1 eleEdw1 triMan1 jacJac1 ochPri3 rn6 sarHar1 apaSpi1 pelSin1 ornAna1 allMis1 colLiv1 galGal4 anaPla1 melGal1 falChe1 falPer1 amaVit1 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 932, context: html, text, full: html, text
• finished myoLuc2 eleEdw1 continuing capHir1 triMan1 chiLan1 eriEur2 mesAur1 micOch1 sorAra2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 45, context: html, text, full: html, text
• v312 final build refs #14821
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v312
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text