File Changes for hiram

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

• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 2, context: html, text, full: html, text
    fix left label offset difficulty refs #9741
    
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Ensembl link could be elsewhere, allow trackDb override default refs #14462
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v312
    
• 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/hg38/lastzRuns.txt
  • lines changed 368, context: html, text, full: html, text
    done with lastz alignments for anoCar2 cheMyd1 chrPic2 xipMac1 punNye1 mayZeb1 danRer10 petMar2 refs #14560
    
  • lines changed 849, context: html, text, full: html, text
    done with oryAfe1 cerSim1 chrAsi1 eptFus1 tupChi1 equCab2 camFer1 vicPac2 turTru2 orcOrc1 speTri2 refs #14560
    
  • lines changed 1408, 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
    
  • lines changed 1155, 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
    
  • lines changed 177, 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
    
  • lines changed 462, context: html, text, full: html, text
    starting rn6 criGri1 mesAur1 micOch1 sorAra2 macEug2 refs #14560
    
  • lines changed 932, 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
    
  • lines changed 45, context: html, text, full: html, text
    finished myoLuc2 eleEdw1 continuing capHir1 triMan1 chiLan1 eriEur2 mesAur1 micOch1 sorAra2 refs #14560
    
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 23, context: html, text, full: html, text
    lastz alignment to panTro4 per user request refs #14793
    
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 1, context: html, text, full: html, text
    tarSyr2 doesn't have any native ESTs don't bother with them refs #14820
    
• src/hg/makeDb/doc/tarSyr2/multiz17way.txt
  • lines changed 17, context: html, text, full: html, text
    forgot to load the phastCons track refs #14410
    
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    remove redundent o_db in the net description refs #14410
    
• src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html
  • lines changed 22, 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
    adding description and placed track in compGeno refs #14278
    
  • lines changed 1, context: html, text, full: html, text
    adding description and placed track in compGeno refs #14278
    
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
  • lines changed 1, context: html, text, full: html, text
    fixup default visibility refs #9741
    
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • lines changed 1, context: html, text, full: html, text
    correct assembly date is July 2007 refs #14835
    
• src/userApps/fetchKentSource.sh
  • lines changed 1, context: html, text, full: html, text
    adding checkUmask.sh to the userApps build fetch refs #14507
    
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    add faAlign to the utils list since it is used in the Ebola construction refs #14278
    
• src/utils/qa/weeklybld/buildEnv.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
    
  • lines changed 3, context: html, text, full: html, text
    v312 final build refs #14821
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 4, 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/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 #14821buildEnv.csh