Commits for hiram
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v285_preview to v285_preview2 (2013-06-04 to 2013-06-11) v285
- adding hgFindSpec and hgTrackDb to the userApps build refs #9149
- updating userApps to make the fetchSource a separate step refs #9149
- src/inc/localEnvironment.mk - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- add the local environment business refs #9149
- add the include localEnvironment.mk to allow build in userApps environment refs #9149
- src/hg/utils/overlapSelect/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/utils/pslMap/makefile - lines changed 4, 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
- src/hg/ratStuff/makefile - lines changed 3, context: html, text, full: html, text
- src/utils/userApps/makefile - lines changed 4, context: html, text, full: html, text
- lastz panTro4 to hg18 refs #10943
- src/hg/makeDb/doc/hg18.txt - lines changed 63, context: html, text, full: html, text
- construct chrom.sizes file after 2bit is done refs #10272
- src/hg/utils/automation/unplacedScaffolds.pl - lines changed 1, context: html, text, full: html, text
- adding takFla1 yellowbelly pufferfish refs #10272
- src/hg/utils/phyloTrees/105way.commonNames.nh - lines changed 105, context: html, text, full: html, text
- src/hg/utils/phyloTrees/105way.nh - lines changed 105, context: html, text, full: html, text
- src/hg/utils/phyloTrees/105way.scientificNames.nh - lines changed 105, context: html, text, full: html, text
- src/hg/utils/phyloTrees/commonNames.sh - lines changed 1, 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 1, context: html, text, full: html, text
- initial files from makeGenomeDb.pl refs #10190
- src/hg/makeDb/trackDb/zebraFinch/taeGut2/description.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebraFinch/taeGut2/gap.html - lines changed 32, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebraFinch/taeGut2/gold.html - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra - lines changed 8, context: html, text, full: html, text
- adding taeGut2 zebra finch to the browser refs #10190
- src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
- better cleaning of RMPart refs #10998
- src/hg/utils/automation/doRepeatMasker.pl - lines changed 8, context: html, text, full: html, text
- adding takFla Takifugu flavidus Yellowbelly puffer fish refs #10272
- src/hg/utils/phyloTrees/vertebrates.txt - lines changed 4, context: html, text, full: html, text
- done with masking ready for genbank refs #10190
- src/hg/makeDb/doc/taeGut2.txt - lines changed 618, context: html, text, full: html, text
- better cleaning of the TrfPart directory refs #10998
- src/hg/utils/automation/doSimpleRepeat.pl - lines changed 3, context: html, text, full: html, text
- adding sorAra2 common shrew refs #9348
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
- starting genbank run refs #9348
- src/hg/makeDb/doc/sorAra2.txt - lines changed 122, context: html, text, full: html, text
- adding taeGut2 Zebra Finch to genbank run refs #10190
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
- adding echTel2 tenrec refs #9693
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
- running genbank refs #9693
- src/hg/makeDb/doc/echTel2.txt - lines changed 47, context: html, text, full: html, text
- fixup echo -e argument situation refs #9149
- indicate an alternative to using git refs #9149
- fixup clean rule so it will function OK without the kent/src directory existing refs #9149
- Added echTel2 to daily hgwdev build refs #9693
- 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
- to add proper description and field labels for the table browser refs #10746
- src/hg/lib/ucscToEnsembl.as - lines changed 6, context: html, text, full: html, text
- initial files from makeGenomeDb.pl refs #9419
- src/hg/makeDb/trackDb/hedgehog/eriEur2/description.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/hedgehog/eriEur2/gap.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/hedgehog/eriEur2/gold.html - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra - lines changed 8, context: html, text, full: html, text
- adding eriEur2 to the build refs #9419
- src/hg/makeDb/trackDb/makefile - lines changed 6, context: html, text, full: html, text
- running masking refs #9419
- src/hg/makeDb/doc/eriEur2.txt - lines changed 1991, context: html, text, full: html, text
- repeat masking finally done with new RM libraries continuing with genscan and cpgIsland builds refs #8750
- src/hg/makeDb/doc/allMis1.txt - lines changed 59, context: html, text, full: html, text
- vicPac1 updates to vicPac2 refs #10272
- src/hg/utils/phyloTrees/105way.nh - lines changed 1, context: html, text, full: html, text
- vicPac1 updates to vicPac2 refs #10272
- src/hg/utils/phyloTrees/commonNames.sh - lines changed 1, context: html, text, full: html, text
- added sorAra2 - shrew - refs #9348
- 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 genbank run refs #9348
- src/hg/makeDb/doc/sorAra2.txt - lines changed 10, context: html, text, full: html, text
- updating allMis0 to allMis1 refs #8750
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 16, context: html, text, full: html, text
- running genbank refs #8750
- src/hg/makeDb/doc/allMis1.txt - lines changed 47, context: html, text, full: html, text
- adding oviAri3 to the browser refs #9409
- src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/sheep/oviAri3/description.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/sheep/oviAri3/gap.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/sheep/oviAri3/gold.html - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra - lines changed 8, context: html, text, full: html, text
- running repeat masker and window masker refs #9409
- src/hg/makeDb/doc/oviAri3.txt - lines changed 597, context: html, text, full: html, text
- adding vicPac2 to the browser refs #10833
- src/hg/makeDb/trackDb/alpaca/vicPac2/description.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/alpaca/vicPac2/gap.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/alpaca/vicPac2/gold.html - lines changed 34, context: html, text, full: html, text
- src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/makefile - lines changed 2, context: html, text, full: html, text
- running repeat masking refs #10833
- src/hg/makeDb/doc/vicPac2.txt - lines changed 2027, context: html, text, full: html, text
- adding oviAri3 Sheep refs #9409
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
- done with masking starting cpgIslands genbank and genscan runs refs #9409
- src/hg/makeDb/doc/oviAri3.txt - lines changed 79, context: html, text, full: html, text
- adding vicPac2 alpaca refs #10833
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 13, context: html, text, full: html, text
- done with masking starting cpgIslands genscan and genbank runs refs #10833
- src/hg/makeDb/doc/vicPac2.txt - lines changed 191, context: html, text, full: html, text
- update cosmic to v65 refs #10158
- src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
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