hiram: changes by file

review to branch (2009-06-02 to 2009-06-09) v208

• src/hg/hgc/hgc.c
  • 1.1550 lines changed: 1, context: html, text, full: html, text
    Proper ATCC URL link for Yeast clones
• src/hg/lib/hVarSubst.c
  • 1.4 lines changed: 47, context: html, text, full: html, text
    Properly look for ClosestToHome variables during substitution and add chain linearGap matrix variable recognition
• src/hg/makeDb/doc/hg19.txt
  • 1.23 lines changed: 69, context: html, text, full: html, text
    the swap lastz are done for those genomes that are public on the RR
  • 1.22 lines changed: 282, context: html, text, full: html, text
    Begin running the swaps
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.52 lines changed: 30, context: html, text, full: html, text
    Fix error for -strict operation, and properly clean up subTracks that had parents disappear
  • 1.51 lines changed: 11, context: html, text, full: html, text
    Properly mark composite parents and children so that ClosestToHome settings will function OK
• src/hg/makeDb/trackDb/humanChainNet.html
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Now showing chain minScore and linearGap options
  • 1.1 lines changed: 151, context: html, text, full: html, text
    Adding hg19 chain and net composite track
• src/hg/makeDb/trackDb/makefile
  • 1.268 lines changed: 1, context: html, text, full: html, text
    Adding canFamPoodle1 to the build, Craig Venter's poodle "Shadow"
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.510 lines changed: 7, context: html, text, full: html, text
    Now showing chain minScore and linearGap options
  • 1.509 lines changed: 37, context: html, text, full: html, text
    Adding hg19 chain and net composite track
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.19 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • 1.23 lines changed: 2, context: html, text, full: html, text
    Add Tasha's name to the photo caption
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Add Tasha's name to the photo caption
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.57 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.14 lines changed: 4, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.38 lines changed: 1, context: html, text, full: html, text
    ATCC clone link now taken care of in hgc.c
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.16 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.37 lines changed: 4, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.19 lines changed: 3, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.51 lines changed: 4, context: html, text, full: html, text
    Add humanChainNet override variables chainMinScore and chainLinearGap
• src/hg/utils/automation/HgAutomate.pm
  • 1.27 lines changed: 15, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/HgRemoteScript.pm
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.29 lines changed: 21, context: html, text, full: html, text
    Find db name from /scratch/data/ directory name, and generalize the ssh command to avoid questions to the shell for new hosts, and properly verify all DEF variables before they start
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.7 lines changed: 8, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/doSimpleRepeat.pl
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makeDownloads.pl
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Generalize the ssh command to avoid questions to the shell for new hosts
• src/hg/utils/automation/makePushQSql.pl
  • 1.25 lines changed: 6, context: html, text, full: html, text
    hgofbeta is now hgsqlbeta, and generalize the ssh command