details: http://www.bx.psu.edu/hg/galaxy/rev/e7d91d58f4ad changeset: 3749:e7d91d58f4ad user: Kelly Vincent <kpvincent@bx.psu.edu> date: Thu May 06 12:11:47 2010 -0400 description: Updated builds.txt (and manual_builds.txt) to newest version, corresponding to that on main. Includes hg19 and phiX correction. diffstat: tool-data/shared/ucsc/builds.txt | 291 +++++++++++++++++-------------- tool-data/shared/ucsc/manual_builds.txt | 2 +- 2 files changed, 160 insertions(+), 133 deletions(-) diffs (355 lines): diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,133 +1,156 @@ #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn ? unspecified (?) -hg18 Human Mar. 2006 (hg18) -hg17 Human May 2004 (hg17) -hg16 Human July 2003 (hg16) -hg15 Human Apr. 2003 (hg15) -hg13 Human Nov. 2002 (hg13) -venter1 J. Craig Venter Sep. 2007 (venter1) -panTro2 Chimp Mar. 2006 (panTro2) -panTro1 Chimp Nov. 2003 (panTro1) -ponAbe2 Orangutan July 2007 (ponAbe2) -rheMac2 Rhesus Jan. 2006 (rheMac2) -calJac1 Marmoset June 2007 (calJac1) -otoGar1 Bushbaby Dec. 2006 (otoGar1) -tupBel1 TreeShrew Dec. 2006 (tupBel1) -mm9 Mouse July 2007 (mm9) -mm8 Mouse Feb. 2006 (mm8) -mm7 Mouse Aug. 2005 (mm7) -mm6 Mouse Mar. 2005 (mm6) -mm5 Mouse May 2004 (mm5) -mm4 Mouse Oct. 2003 (mm4) -mm3 Mouse Feb. 2003 (mm3) -mm2 Mouse Feb. 2002 (mm2) -rn4 Rat Nov. 2004 (rn4) -rn3 Rat June 2003 (rn3) -rn2 Rat Jan. 2003 (rn2) -oryCun1 Rabbit May 2005 (oryCun1) -felCat3 Cat Mar. 2006 (felCat3) -canFam2 Dog May 2005 (canFam2) -canFam1 Dog July 2004 (canFam1) -equCab1 Horse Jan. 2007 (equCab1) -bosTau4 Cow Oct. 2007 (bosTau4) -bosTau3 Cow Aug. 2006 (bosTau3) -bosTau2 Cow Mar. 2005 (bosTau2) -bosTau1 Cow Sep. 2004 (bosTau1) -choHof1 Sloth Feb. 2008 (choHof1) -dasNov1 Armadillo May 2005 (dasNov1) -echTel1 Tenrec July 2005 (echTel1) -loxAfr1 Elephant May 2005 (loxAfr1) -monDom4 Opossum Jan. 2006 (monDom4) -monDom1 Opossum Oct. 2004 (monDom1) -ornAna1 Platypus Mar. 2007 (ornAna1) -galGal3 Chicken May 2006 (galGal3) -galGal2 Chicken Feb. 2004 (galGal2) -anoCar1 Lizard Feb. 2007 (anoCar1) -xenTro2 X. tropicalis Aug. 2005 (xenTro2) -xenTro1 X. tropicalis Oct. 2004 (xenTro1) -danRer5 Zebrafish July 2007 (danRer5) -danRer4 Zebrafish Mar. 2006 (danRer4) -danRer3 Zebrafish May 2005 (danRer3) -danRer2 Zebrafish June 2004 (danRer2) -danRer1 Zebrafish Nov. 2003 (danRer1) -tetNig1 Tetraodon Feb. 2004 (tetNig1) -fr2 Fugu Oct. 2004 (fr2) -fr1 Fugu Aug. 2002 (fr1) -gasAcu1 Stickleback Feb. 2006 (gasAcu1) -oryLat1 Medaka Apr. 2006 (oryLat1) -petMar1 Lamprey Mar. 2007 (petMar1) -borEut13 Boreoeutherian Apr. 24. 2006 (borEut13) -canHg12 Boreoeutherian Nov. 19. 2005 (canHg12) -rodEnt13 Rodent Apr. 24. 2006 (rodEnt13) -priMat13 Primate Apr. 24. 2006 (priMat13) -nonAfr13 Non-Afrotheria Apr. 24. 2006 (nonAfr13) -lauRas13 Laurasiatheria Apr. 24. 2006 (lauRas13) -homIni14 Hominidae Oct. 1. 2006 (homIni14) -homIni13 Hominidae Apr. 24. 2006 (homIni13) -gliRes13 Glires Apr. 24. 2006 (gliRes13) -eutHer13 Eutheria Apr. 24. 2006 (eutHer13) -euaGli13 Euarchontoglires Apr. 24. 2006 (euaGli13) -catArr1 Catarrhini June 13. 2006 (catArr1) -afrOth13 Afrotheria Apr. 24. 2006 (afrOth13) -braFlo1 Lancelet Mar. 2006 (braFlo1) -ci2 C. intestinalis Mar. 2005 (ci2) -ci1 C. intestinalis Dec. 2002 (ci1) -cioSav2 C. savignyi July 2005 (cioSav2) -cioSav1 C. savignyi Sept. 2001 (cioSav1) -strPur2 S. purpuratus Sep. 2006 (strPur2) -strPur1 S. purpuratus Apr. 2005 (strPur1) -ce4 C. elegans Jan. 2007 (ce4) -ce3 C. elegans March 2005 (ce3) -ce2 C. elegans Mar. 2004 (ce2) -ce1 C. elegans May 2003 (ce1) -caePb1 C. brenneri Jan. 2007 (caePb1) -cb3 C. briggsae Jan. 2007 (cb3) -cb2 C. briggsae Aug 2005 (cb2) -cb1 C. briggsae July 2002 (cb1) -caeRem2 C. remanei Mar. 2006 (caeRem2) -caeRem1 C. remanei March 2005 (caeRem1) -priPac1 P. pacificus Feb. 2007 (priPac1) -dm3 D. melanogaster Apr. 2006 (dm3) -dm2 D. melanogaster Apr. 2004 (dm2) -dm1 D. melanogaster Jan. 2003 (dm1) -droSim1 D. simulans Apr. 2005 (droSim1) -droSec1 D. sechellia Oct. 2005 (droSec1) -droYak2 D. yakuba Nov. 2005 (droYak2) -droYak1 D. yakuba Apr. 2004 (droYak1) -droEre1 D. erecta Aug. 2005 (droEre1) -droAna2 D. ananassae Aug. 2005 (droAna2) -droAna1 D. ananassae July 2004 (droAna1) -dp3 D. pseudoobscura Nov. 2004 (dp3) -dp2 D. pseudoobscura Aug. 2003 (dp2) -droPer1 D. persimilis Oct. 2005 (droPer1) -droVir2 D. virilis Aug. 2005 (droVir2) -droVir1 D. virilis July 2004 (droVir1) -droMoj2 D. mojavensis Aug. 2005 (droMoj2) -droMoj1 D. mojavensis Aug. 2004 (droMoj1) -droGri1 D. grimshawi Aug. 2005 (droGri1) -anoGam1 A. gambiae Feb. 2003 (anoGam1) -apiMel2 A. mellifera Jan. 2005 (apiMel2) -apiMel1 A. mellifera July 2004 (apiMel1) -triCas2 T. castaneum Sep. 2005 (triCas2) -falciparum P. falciparum Plasmodium falciparum (falciparum) -sacCer1 S. cerevisiae Oct. 2003 (sacCer1) -sc1 SARS coronavirus Apr. 2003 (sc1) -campJeju1 Campylobacter jejuni 02/25/2000 (campJeju1) -campJeju_RM1221_1 Campylobacter jejuni RM1221 01/07/2005 (campJeju_RM1221_1) -eschColi_CFT073_1 Escherichia coli CFT073 12/10/2002 (eschColi_CFT073_1) -eschColi_K12_1 Escherichia coli K12 09/05/1997 (eschColi_K12_1) -eschColi_O157H7_1 Escherichia coli O157H7 03/29/2000 (eschColi_O157H7_1) -eschColi_O157H7EDL933_1 Escherichia coli O157H7 EDL933 02/24/2001 (eschColi_O157H7EDL933_1) -vibrChol1 Vibrio cholerae O1 El Tor 08/22/2000 (vibrChol1) -vibrChol_MO10_1 Vibrio cholerae MO10 09/17/2005 (vibrChol_MO10_1) -vibrChol_O395_1 Vibrio cholerae O395 09/17/2005 (vibrChol_O395_1) -vibrFisc_ES114_1 Vibrio fischeri ES114 02/11/2005 (vibrFisc_ES114_1) -vibrPara1 Vibrio parahaemolyticus 06/02/2000 (vibrPara1) -vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 09/23/2003 (vibrVuln_CMCP6_1) -vibrVuln_YJ016_1 Vibrio vulnificus YJ016 12/06/2003 (vibrVuln_YJ016_1) -heliHepa1 Helicobacter hepaticus 06/18/2003 (heliHepa1) -heliPylo_26695_1 Helicobacter pylori 26695 08/07/1997 (heliPylo_26695_1) -heliPylo_J99_1 Helicobacter pylori J99 01/29/1999 (heliPylo_J99_1) +hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +hg16 Human July 2003 (NCBI34/hg16) (hg16) +hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) +venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) +gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) +gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) +micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) +tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) +mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) +homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) +homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) +sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) +speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) +ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) +eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) +felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +canFam1 Dog July 2004 (Broad/canFam1) (canFam1) +canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) +myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) +susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) +turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) +tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) +proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) +choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) +bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) +macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) +dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) +dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) +echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) +loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) +danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) +danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) +canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) +rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) +priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) +nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) +lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) +homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) +homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) +gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) +eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) +euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) +catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) +afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) +cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) +ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +ce3 C. elegans March 2005 (WS140/ce3) (ce3) +ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) +caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) +falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) +sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) +sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) +phiX phiX174 (phiX) 16079 Mycobacterium sp. JLS (16079) symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 (symbTher_IAM14863) 16070 Yersinia pseudotuberculosis IP 31758 (16070) @@ -356,6 +379,7 @@ 16062 Leuconostoc citreum KM20 (16062) 16148 Leptospira borgpetersenii serovar Hardjo-bovis JB197 (16148) 16146 Leptospira borgpetersenii serovar Hardjo-bovis L550 (16146) +vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 (vibrVuln_CMCP6_1) 10877 Bacillus thuringiensis serovar konkukian str. 97-27 (10877) 19517 Clostridium botulinum A str. ATCC 19397 (19517) nitrWino_NB_255 Nitrobacter winogradskyi Nb-255 (nitrWino_NB_255) @@ -500,6 +524,7 @@ 28507 Clostridium botulinum A3 str. Loch Maree (28507) colwPsyc_34H Colwellia psychrerythraea 34H (colwPsyc_34H) hyphNept_ATCC15444 Hyphomonas neptunium ATCC 15444 (hyphNept_ATCC15444) +vibrChol1 Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) deinGeot_DSM11300 Deinococcus geothermalis DSM 11300 (deinGeot_DSM11300) 312 Buchnera aphidicola str. Sg (Schizaphis graminum) (312) 311 Streptococcus pyogenes MGAS315 (311) @@ -536,6 +561,7 @@ 12720 Enterobacter sakazakii ATCC BAA-894 (12720) therMari Thermotoga maritima MSB8 (therMari) mycoGeni Mycoplasma genitalium G37 (mycoGeni) +vibrFisc_ES114_1 Vibrio fischeri ES114 (vibrFisc_ES114_1) pyroIsla1 Pyrobaculum islandicum DSM 4184 (pyroIsla1) 17407 Burkholderia multivorans ATCC 17616 (17407) 13030 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- (13030) @@ -544,6 +570,7 @@ 19857 Vibrio harveyi ATCC BAA-1116 (19857) 17639 Parvibaculum lavamentivorans DS-1 (17639) 18059 Mycobacterium bovis BCG str. Pasteur 1173P2 (18059) +vibrPara1 Vibrio parahaemolyticus RIMD 2210633 (vibrPara1) 259 Escherichia coli O157:H7 EDL933 (259) 64 Staphylococcus epidermidis RP62A (64) neisGono_FA1090_1 Neisseria gonorrhoeae FA 1090 (neisGono_FA1090_1) @@ -598,6 +625,7 @@ vermEise_EF01_2 Verminephrobacter eiseniae EF01-2 (vermEise_EF01_2) granBeth_CGDNIH1 Granulibacter bethesdensis CGDNIH1 (granBeth_CGDNIH1) alcaBork_SK2 Alcanivorax borkumensis SK2 (alcaBork_SK2) +vibrChol_O395_1 Vibrio cholerae O395 (vibrChol_O395_1) nitrOcea_ATCC19707 Nitrosococcus oceani ATCC 19707 (nitrOcea_ATCC19707) campJeju_RM1221 Campylobacter jejuni RM1221 (campJeju_RM1221) 12468 Bacillus cereus E33L (12468) @@ -723,6 +751,7 @@ 12637 Clostridium beijerinckii NCIMB 8052 (12637) ehrlRumi_WELGEVONDEN Ehrlichia ruminantium str. Welgevonden (ehrlRumi_WELGEVONDEN) methLabrZ_1 Methanocorpusculum labreanum Z (methLabrZ_1) +vibrVuln_YJ016_1 Vibrio vulnificus YJ016 (vibrVuln_YJ016_1) 13773 Streptococcus thermophilus LMD-9 (13773) 20039 Leptothrix cholodnii SP-6 (20039) shewAmaz Shewanella amazonensis SB2B (shewAmaz) @@ -786,7 +815,5 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) shewOnei Shewanella oneidensis MR-1 (shewOnei) -equCab2 Horse Sep. 2007 (equCab2) -arabidopsis Arabidopsis thaliana TAIR9 -arabidopsis_tair8 Arabidopsis thaliana TAIR8 -araTha1 Arabidopsis thaliana TAIR7 +15217 Human herpesvirus 1 (15217) +lMaj5 Leishmania major 2005 (lMaj5) diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,4 +1,4 @@ -phix phiX174 phix=5386 +phiX phiX174 phiX=5386 16079 Mycobacterium sp. JLS NC_009077=6048425 symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 chr=3566135 16070 Yersinia pseudotuberculosis IP 31758 NC_009708=4723306,NC_009705=153140,NC_009704=58679