Commits for hiram

v286_preview to v286_preview2 (2013-06-24 to 2013-07-02) v286

• better cleaning of the TrfPart directory refs #10998
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 1, context: html, text, full: html, text
• ready for v286 with the beta branch fetch instead of HEAD refs #9149
  • src/userApps/fetchKentSource.sh - lines changed 10, context: html, text, full: html, text
• adding xenTro7 Xenopus (Silurana) tropicalis refs #9868
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 21, context: html, text, full: html, text
• starting genbank refs #9868
  • src/hg/makeDb/doc/xenTro7.txt - lines changed 86, context: html, text, full: html, text
• liftOver taeGut1 to taeGut2 refs #10190
  • src/hg/makeDb/doc/taeGut1.txt - lines changed 20, context: html, text, full: html, text
• liftOver eriEur1 to eriEur2 refs #9419
  • src/hg/makeDb/doc/eriEur1.txt - lines changed 20, context: html, text, full: html, text
• wrapping up lastz for echTel2 oviAri3 sorAra2 and starting lastz zonAlb2 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 86, context: html, text, full: html, text
• done with genbank and blatServers entries refs #8750
  • src/hg/makeDb/doc/allMis1.txt - lines changed 17, context: html, text, full: html, text
• done with genscan and lastz to mouse mm10 refs #9693
  • src/hg/makeDb/doc/echTel2.txt - lines changed 1677, context: html, text, full: html, text
• running lastz to vicPac2 refs #10833
  • src/hg/makeDb/doc/mm10.txt - lines changed 65, context: html, text, full: html, text
• done with lastz for zonAlb1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 31, context: html, text, full: html, text
• done with zonAlb1 lastz starting falChe1 falPer1 anaPla1 amaVit1 melUnd1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 332, context: html, text, full: html, text
• adjusting default visibilities refs #8750
  • src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra - lines changed 27, context: html, text, full: html, text
• finishing up lastz for echTel2 oviAri3 falChe1 falPer1 anaPla1 amaVit1 allMis1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 124, context: html, text, full: html, text
• liftOver to oviAri3 refs #9409
  • src/hg/makeDb/doc/oviAri1.txt - lines changed 19, context: html, text, full: html, text
• ready for all.joiner downloads and pushQ refs #9409
  • src/hg/makeDb/doc/oviAri3.txt - lines changed 102, context: html, text, full: html, text
• done with melUnd1 lastz refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• done with falChe1 lastz refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
• setting default track visibilities refs #9693
  • src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra - lines changed 18, context: html, text, full: html, text
• in the pushQ 007047 refs #9693
  • src/hg/makeDb/doc/echTel2.txt - lines changed 12, context: html, text, full: html, text
• in the pushQ 007047 refs #9693
  • src/hg/makeDb/doc/echTel2.txt - lines changed 3, context: html, text, full: html, text
• in the pushQ 007048 refs #10833
  • src/hg/makeDb/doc/vicPac2.txt - lines changed 1676, context: html, text, full: html, text
• adding macFas5 chlSab1 araMac1 refs #10272
  • src/hg/utils/phyloTrees/108way.commonNames.nh - lines changed 108, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/108way.nh - lines changed 108, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/108way.scientificNames.nh - lines changed 108, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 3, context: html, text, full: html, text
• starting lastz for colLiv1 ficAlb2 araMac1 galGal4 pseHum1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 330, context: html, text, full: html, text
• done with lastz for pseHum1 ficAlb2 colLiv1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
• done with lastz for araMac1 and galGal4 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• starting lastz on chlSab1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 59, context: html, text, full: html, text
• starting lastz on macFas3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 72, context: html, text, full: html, text
• starting lastz on saiBol1 and otoGar3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 124, context: html, text, full: html, text
• Added xenTro7. refs #9868
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• fix eriEur2 hedgehog entry for ooc file refs #9419
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• finishing off lastz for ochPri3 oviAri3 macFas5 saiBol1 otoGar3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 87, context: html, text, full: html, text
• done with lastz for allMis1 macFas5 ochPri3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 21, context: html, text, full: html, text
• Added taeGut2. refs #10190
  • 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
• Added eriEur2 to daily hgwdev build refs #9419
  • 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
• running up swap lastz for tarSyr1 papHam1 tupBel1 pteVam1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 77, context: html, text, full: html, text
• allow contig names to translate also refs #11114
  • src/hg/utils/automation/ensGeneScaffolds.pl - lines changed 1, context: html, text, full: html, text