pchan: changes by file

review to branch (2009-10-06 to 2009-10-13) v217

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.86 lines changed: 33, context: html, text, full: html, text
    add haloVolc1_1 from Halolex
• src/hg/archaeStuff/data/private-genomes.tab
  • 1.3 lines changed: 16, context: html, text, full: html, text
    add haloferax private browser and haloVolc1_1 as private genome
  • 1.2 lines changed: 14, context: html, text, full: html, text
    mark all private genomes as private to haloferax collab browser
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.50 lines changed: 5, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.49 lines changed: 11, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.26 lines changed: 21, context: html, text, full: html, text
    make more coding changes to support annotRev in Blastp
  • 1.25 lines changed: 36, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.24 lines changed: 158, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm
  • 1.20 lines changed: 35, context: html, text, full: html, text
    make more coding changes to support annotRev in Blastp
  • 1.19 lines changed: 325, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.37 lines changed: 4, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.36 lines changed: 72, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.45 lines changed: 3, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.44 lines changed: 102, context: html, text, full: html, text
    read private-genomes.tab to skip sync'ing and initdb; add --removepriv to clean up hits to private genomes in blastp, blastx, and alignFeatures tracks
• src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fix bug when cleaning up data in collab server; add --annotrev for revised annotation track; add annotRev list to description page
  • 1.1 lines changed: 196, context: html, text, full: html, text
    add -removepriv to clean up private genome hits
• src/hg/lib/alignInfo.sql
  • 1.1 lines changed: 21, context: html, text, full: html, text
    created by Andrew Holmes for lowelab alignment feature track
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.14 lines changed: 2, context: html, text, full: html, text
    add annotRev list to description page
• src/hg/makeDb/trackDb/lowelab/halMar1/trackDb.ra
  • 1.18 lines changed: 22, context: html, text, full: html, text
    comment out chainHalMar1 and blastzHalMar1
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
  • 1.22 lines changed: 23, context: html, text, full: html, text
    comment out chainHalMar1 and blastzHalMar1
• src/hg/makeDb/trackDb/lowelab/haloVolc1_1/trackDb.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Update annotRev track
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Update annotRev track
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Update annotRev track
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Update annotRev track
• src/hg/makeDb/trackDb/lowelab/peloCarb/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    delete old multiz track
• src/hg/makeDb/trackDb/lowelab/peloProp_DSM2379/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    delete old multiz track