Commits for hiram

v312_base to v313_preview (2015-02-16 to 2015-02-23) v313

• completed capHir1 triMan1 conCri1 apaSpi1 redone rn6 micOch1 swapping criGri1 sorAra2 macEug2 sarhar1 pelSin1 ornAna1 allMis1 colLiv1 anaPla1 melGal1 falChe1 amaVit refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 137, context: html, text, full: html, text
• finished: rn6 criGri1 mesAur1 sorAra2 sarHar1 alMis1 colLiv1 galGal4 melGal1 falChe1 falPer1 running micOch1 macEug2 apaSpi1 ornAna1 anaPla1 amaVit1 araMac1 pseHum1 melUnd1 ficAlb2 zonAlb1 geoFor1 taeGut2 gadMor1 gasAcu1 oreNil2 tetNig2 neoBri1 takFla1 hapBur1 fr3 astMex refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 1268, context: html, text, full: html, text
• begin reruns on chrAsi1 criGri1 eleEdw1 eriEur2 jacJac1 macEug2 mesAur1 sorAra2 tupChi1 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 178, context: html, text, full: html, text
• Added nasLar1 - Proboscis monkey refs #14437
  
  • 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
• adding nasLar1 refs #14437
  
  • src/hg/makeDb/schema/all.joiner - lines changed 11, context: html, text, full: html, text
• add newSequences track tables to tables ignored for eboVir3 refs #14278
  
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• add rules for hg38Patch2 tracks refs #14167
  
  • src/hg/makeDb/schema/all.joiner - lines changed 7, context: html, text, full: html, text
• nasLar1 in the pushQ refs #14437
  
  • src/hg/makeDb/doc/nasLar1/initialBuild.txt - lines changed 546, context: html, text, full: html, text
  • src/hg/makeDb/doc/nasLar1/ucscCompositeAgp.pl - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/doc/nasLar1/unplaced.pl - lines changed 48, context: html, text, full: html, text
• done with araMac1 gasAcu1 tetNig2 neoBri1 takFla1 hapBur1 fr3 continuing oreNil2 xenTro7 latCha1 lepOcu1 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 286, context: html, text, full: html, text
• now using the correct sequence for this build refs #14438
  
  • src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/gold.html - lines changed 2, context: html, text, full: html, text
• using dev/random to generate seed to drand48 to obtain random strings refs #14863
  
  • src/oneShot/randString/makefile - lines changed 3, context: html, text, full: html, text
  • src/oneShot/randString/randString.c - lines changed 82, context: html, text, full: html, text
• rerun alignments for chrAsi1 eptFus1 tupChi1 equCab2 eleEdw1 jacJac1 eriEur2 echTel2 mesAur1 sorAra2 macEug2 and done with sarHar1 ornAna1 melGal1 pseHum1 melUnd1 ficAlb2 zonAlb1 geoFor1 taeGut2 gadMor1 gasAcu1 tetNig2 xenTro7 latCha1 lepOcu1refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 199, context: html, text, full: html, text
• adding <db>.chrom.sizes to the bigZips downloads refs #11248
  
  • src/hg/utils/automation/makeDownloads.pl - lines changed 6, context: html, text, full: html, text
• Added rhiRox1; refs #14438
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 22, context: html, text, full: html, text
• Added rhiRox Rhinopithecus roxellana refs #14438
  
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• Added rhiRox1 - Golden snub-nosed monkey refs #14438
  
  • 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
• done with rerun of criGri1 and done with macEug2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 13, context: html, text, full: html, text
• v313 preview1 refs #14821
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text