File Changes for hiram

v285_base to v286_preview (2013-06-18 to 2013-06-24) v286

• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add localEnvironment.mk include so local makes can work here for userApps refs #9149
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 28, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 82, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 19, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 342, context: html, text, full: html, text
    running lastz runs for ochPri3 oviAri3 sorAra2 taeGut2 vicPac2 refs #9347 #9409 #9348 #10190 #10833
  • lines changed 42, context: html, text, full: html, text
    running lastz runs for ochPri3 oviAri3 sorAra2 taeGut2 vicPac2 refs #9347 #9409 #9348 #10190 #10833
• src/hg/makeDb/doc/loxAfr1.txt
  • lines changed 21, context: html, text, full: html, text
    construct liftOvers to loxAfr3 refs #11064
• src/hg/makeDb/doc/loxAfr2.txt
  • lines changed 21, context: html, text, full: html, text
    construct liftOvers to loxAfr3 refs #11064
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/mm10.txt
  • lines changed 130, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 2074, context: html, text, full: html, text
    running masking refs #9347
  • lines changed 48, context: html, text, full: html, text
    masking done starting genscan cpgIslands and ready for genbank refs #9347
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 20, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/rn5.txt
  • lines changed 43, context: html, text, full: html, text
    prompted NCBI to fix the rn5 cytoband file, load up cytoBand and Ideo refs #8529
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 73, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added vicPac2 to daily hgwdev build refs #10833
  • lines changed 1, context: html, text, full: html, text
    Added oviAri3. refs #9409
  • lines changed 1, context: html, text, full: html, text
    Added allMis1 refs #8750
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding eriEur2 hedgehog refs #9419
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added vicPac2 to daily hgwdev build refs #10833
  • lines changed 1, context: html, text, full: html, text
    Added oviAri3. refs #9409
  • lines changed 1, context: html, text, full: html, text
    Added allMis1 refs #8750
• src/hg/makeDb/schema/all.joiner
  • lines changed 17, context: html, text, full: html, text
    adding vicPac2 rules refs #10833
  • lines changed 11, context: html, text, full: html, text
    adding allMis1 rules refs #8750
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    adding pika/ochPri3 to the build refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/description.html
  • lines changed 63, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 197, context: html, text, full: html, text
    adding ensGene v72 definitions, suspiciously identical to v71, refs #11114
• src/inc/common.mk
  • lines changed 15, context: html, text, full: html, text
    add new rules for finding mysql as found by compiling on beer30 refs #9149
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add localEnvironment.mk include so local makes can work here for userApps refs #9149