File Changes for hiram

v285_preview to v285_preview2 (2013-06-04 to 2013-06-11) v285

• src/hg/lib/ucscToEnsembl.as
  • lines changed 6, context: html, text, full: html, text
    to add proper description and field labels for the table browser refs #10746
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 59, context: html, text, full: html, text
    repeat masking finally done with new RM libraries continuing with genscan and cpgIsland builds refs #8750
  • lines changed 47, context: html, text, full: html, text
    running genbank refs #8750
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 47, context: html, text, full: html, text
    running genbank refs #9693
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 1991, context: html, text, full: html, text
    running masking refs #9419
• src/hg/makeDb/doc/hg18.txt
  • lines changed 63, context: html, text, full: html, text
    lastz panTro4 to hg18 refs #10943
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v65 refs #10158
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 597, context: html, text, full: html, text
    running repeat masker and window masker refs #9409
  • lines changed 79, context: html, text, full: html, text
    done with masking starting cpgIslands genbank and genscan runs refs #9409
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 122, context: html, text, full: html, text
    starting genbank run refs #9348
  • lines changed 10, context: html, text, full: html, text
    done with genbank run refs #9348
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 618, context: html, text, full: html, text
    done with masking ready for genbank refs #10190
• src/hg/makeDb/doc/vicPac2.txt
  • lines changed 2027, context: html, text, full: html, text
    running repeat masking refs #10833
  • lines changed 191, context: html, text, full: html, text
    done with masking starting cpgIslands genscan and genbank runs refs #10833
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 to daily hgwdev build refs #9693
  • lines changed 1, context: html, text, full: html, text
    added sorAra2 - shrew - refs #9348
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding sorAra2 common shrew refs #9348
  • lines changed 17, context: html, text, full: html, text
    adding taeGut2 Zebra Finch to genbank run refs #10190
  • lines changed 19, context: html, text, full: html, text
    adding echTel2 tenrec refs #9693
  • lines changed 16, context: html, text, full: html, text
    updating allMis0 to allMis1 refs #8750
  • lines changed 19, context: html, text, full: html, text
    adding oviAri3 Sheep refs #9409
  • lines changed 13, context: html, text, full: html, text
    adding vicPac2 alpaca refs #10833
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 to daily hgwdev build refs #9693
  • lines changed 1, context: html, text, full: html, text
    added sorAra2 - shrew - refs #9348
• src/hg/makeDb/makefile
  • lines changed 4, context: html, text, full: html, text
    adding hgFindSpec and hgTrackDb to the userApps build refs #9149
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/makeDb/trackDb/alpaca/vicPac2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/hedgehog/eriEur2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #9419
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding taeGut2 zebra finch to the browser refs #10190
  • lines changed 6, context: html, text, full: html, text
    adding eriEur2 to the build refs #9419
  • lines changed 1, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
  • lines changed 2, context: html, text, full: html, text
    adding vicPac2 to the browser refs #10833
• src/hg/makeDb/trackDb/sheep/oviAri3/description.html
  • lines changed 63, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding oviAri3 to the browser refs #9409
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #10190
• src/hg/makefile
  • lines changed 3, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/mouseStuff/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/ratStuff/makefile
  • lines changed 3, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 8, context: html, text, full: html, text
    better cleaning of RMPart refs #10998
• src/hg/utils/automation/doSimpleRepeat.pl
  • lines changed 3, context: html, text, full: html, text
    better cleaning of the TrfPart directory refs #10998
• src/hg/utils/automation/unplacedScaffolds.pl
  • lines changed 1, context: html, text, full: html, text
    construct chrom.sizes file after 2bit is done refs #10272
• src/hg/utils/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/hg/utils/overlapSelect/makefile
  • lines changed 4, context: html, text, full: html, text
    add the include localEnvironment.mk to allow build in userApps environment refs #9149
• src/hg/utils/phyloTrees/105way.commonNames.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/105way.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
  • lines changed 1, context: html, text, full: html, text
    vicPac1 updates to vicPac2 refs #10272
• src/hg/utils/phyloTrees/105way.scientificNames.nh
  • lines changed 105, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
  • lines changed 1, context: html, text, full: html, text
    vicPac1 updates to vicPac2 refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 8, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding takFla1 yellowbelly pufferfish refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 4, context: html, text, full: html, text
    adding takFla Takifugu flavidus Yellowbelly puffer fish refs #10272
• src/hg/utils/pslMap/makefile
  • lines changed 4, context: html, text, full: html, text
    add the include localEnvironment.mk to allow build in userApps environment refs #9149
• src/inc/localEnvironment.mk
  • lines changed 0, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
• src/inc/userApp.mk
  • lines changed 1, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/userApps/Makefile
  • lines changed 23, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
  • lines changed 18, context: html, text, full: html, text
    add the local environment business refs #9149
  • lines changed 4, context: html, text, full: html, text
    fixup echo -e argument situation refs #9149
  • lines changed 2, context: html, text, full: html, text
    indicate an alternative to using git refs #9149
  • lines changed 1, context: html, text, full: html, text
    fixup clean rule so it will function OK without the kent/src directory existing refs #9149
• src/userApps/README
  • lines changed 1, context: html, text, full: html, text
    updating userApps to make the fetchSource a separate step refs #9149
  • lines changed 29, context: html, text, full: html, text
    indicate an alternative to using git refs #9149
• src/utils/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149
• src/utils/userApps/makefile
  • lines changed 4, context: html, text, full: html, text
    including localEnvironment.mk to allow function in userApp environment refs #9149