hiram: changes by commit

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

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