Commits for hiram

v348_preview to v348_preview2 (2017-04-10 to 2017-04-17) v348

d5da065c768d497f0452ff83be950cd63b288df1 Tue Apr 11 07:22:20 2017 -0700

• chrPic2 does not need to be release alpha refs #19151
  • src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra - lines changed 5, context: html, text, full: html, text

cb5fef38b627bcad929a5f437a2868f5289dd67b Tue Apr 11 11:09:45 2017 -0700

• running up db build refs #19228
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 806, context: html, text, full: html, text

dfab6e0f4db8c5a6c978c50bea07959e71a9546a Tue Apr 11 12:44:33 2017 -0700

• photo micrograph image of cells via WikiMedia Commons user Alcibiades refs #19228
  • src/hg/htdocs/images/Cricetulus_griseus_CHO_cell_line.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

9f3841ee085a633687246a4519ab9e8df4834a3e Tue Apr 11 12:53:52 2017 -0700

• correct line break on BioProject line refs #19338
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 1, context: html, text, full: html, text

377a1cdd03c1dad8578976bb8b8deea13a148ac3 Tue Apr 11 13:32:35 2017 -0700

• add correct line break for BioProject, BioSample lines refs #19228
  • src/hg/makeDb/trackDb/alpaca/vicPac1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/alpaca/vicPac2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/armadillo/dasNov3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papHam1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/balAcu/balAcu1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bats/rouAeg1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/amaVit1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/aptMan1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/aquChr2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/melUnd1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bison/bisBis1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat8/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ciliate/oxyTri2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau7/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau8/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGri1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droSim2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/bunEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/marVir1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/taiEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ferret/musFur1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/frog/nanPar1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gadMor/gadMor1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gator/allMis1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19Patch9/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38Patch7/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38Patch9/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/braFlo2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/latCha/latCha1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macNem1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/manatee/triMan1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/megabat/pteVam1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/micOch/micOch1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10Patch1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10Patch4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10Strains1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oreNil/oreNil2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pangolin/manPen1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pika/ochPri2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pika/ochPri3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/plasFalc3D7/plasFalc3D7V12/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/poeRet/poeRet1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/proboscis/nasLar1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/reptiles/thaSir1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac7/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhino/cerSim1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sheep/oviAri3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sloth/choHof1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr1/description.html - lines changed 1, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tenrec/echTel1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tenrec/echTel2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turtle/chrPic1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turtle/chrPic2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/whale/orcOrc1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ancCey1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ascSuu1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/description.html - lines changed 1, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/worm/caeAng2/description.html - lines changed 1, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/worm/ce11/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/haeCon2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/hetBac1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melInc2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/necAme1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/panRed1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priExs1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/priPac3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro7/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro9/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebraFinch/taeGut2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer10/description.html - lines changed 1, context: html, text, full: html, text

87502d1e3c7819d4ffeba0d87838f60ad46340c4 Tue Apr 11 13:34:50 2017 -0700

• adding criGriChoV1 to the build refs #19228
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

2941ddf2b9652a81511515bf8957506f80aec793 Tue Apr 11 14:14:16 2017 -0700

• adding gold table assembly track search rule refs #19228
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 5, context: html, text, full: html, text

65d33b6223953c4153f2f1ce79cc8a5c5e809e3c Tue Apr 11 14:19:59 2017 -0700

• running up repeat masker and simpleRepeats refs #19228
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 52, context: html, text, full: html, text

01a04be3617875a837371d4fca79da230de27997 Thu Apr 13 10:49:55 2017 -0700

• adding criGriChoV1 Cricetulus griseus - Chinese hamster ovary cell line CHO-K1 refs #19228
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

5ccbeeee1b8c10441197297ae1c5d1c196cc42ea Thu Apr 13 11:40:37 2017 -0700

• adding contigOverlaps track definition and description refs #19228
  • src/hg/makeDb/trackDb/contigOverlaps.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 6, context: html, text, full: html, text

d386116a7da726ae00e8b8366b300c8858431fe1 Thu Apr 13 12:48:03 2017 -0700

• masking done, running up genbank and other tracks refs #19338
  • src/hg/makeDb/doc/criGriChoV1/initialBuild.txt - lines changed 114, context: html, text, full: html, text

0ae2ba6606bb4b40fbeea2ce5e4b6215d752ae2e Fri Apr 14 07:07:30 2017 -0700

• adding chainNet for criGriChoV1 refs #19228
  • src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra - lines changed 51, context: html, text, full: html, text

00845517a81110e655e0ba58b0e697d64edd73c0 Fri Apr 14 07:20:29 2017 -0700

• fixup compile error refs #18736
  • src/hg/lib/barChartUi.c - lines changed 1, context: html, text, full: html, text

609375c3348c52ee3ef7cb0530357c27b0da1d9a Fri Apr 14 10:25:58 2017 -0700

• working up scripts to run of gap overlaps track refs #19338
  • src/hg/utils/automation/nBedToEnds.pl - lines changed 89, context: html, text, full: html, text

9c90d726532203934ba8cf98f63aa479c4a66baf Fri Apr 14 11:41:44 2017 -0700

• working up scripts to run of gap overlaps track refs #19338
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 291, context: html, text, full: html, text

35bb5aff54aacd1fe8c62f04919a2f2aac594051 Fri Apr 14 13:24:20 2017 -0700

• working up scripts to run of gap overlaps track refs #19338
  • src/hg/utils/automation/overlapPslToBed.pl - lines changed 40, context: html, text, full: html, text

b999fc41483f03800f162760724d2897a122237b Fri Apr 14 14:41:48 2017 -0700

• contigOverlaps better named gapOverlap refs #19228
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 3, context: html, text, full: html, text

ce17fa8c5d10cee630ba8b7cc78072d7caaf6e09 Fri Apr 14 14:50:46 2017 -0700

• might be done refs #19338
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 65, context: html, text, full: html, text

33f9582d6589aacd1c18f5cecda35355484546fd Fri Apr 14 14:52:14 2017 -0700

• might be done refs #19338
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 1, context: html, text, full: html, text

5daaa11431460f78caab1530a38c5d11c3cde35c Fri Apr 14 15:00:33 2017 -0700

• correctly collect psl results refs #19338
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 1, context: html, text, full: html, text

845134e6017c4481340920f766378cf92d4977a1 Mon Apr 17 09:59:30 2017 -0700

• v348 preview2 refs #19231
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text