hiram: changes by commit

branch to review (2010-02-02 to 2010-02-10) v225

• Clean up pslUniq and place it into the build
  • src/hg/utils/pslUniq/pslUniq.c 1.4 - lines changed: 8, context: html, text, full: html, text
• the extra ; in the comment causes it to be invalid SQL ?
  • src/hg/lib/simpleRepeat.sql 1.9 - lines changed: 1, context: html, text, full: html, text
• fixup usage of AGP files with comments and FASTA with Genbank ID lines
  • src/hg/utils/automation/makeGenomeDb.pl 1.26 - lines changed: 11, context: html, text, full: html, text
• allow use of lastz or blastz directory
  • src/hg/utils/automation/doRecipBest.pl 1.12 - lines changed: 9, context: html, text, full: html, text
• Downloading new Marmoset assembly
  • src/hg/makeDb/doc/calJac3.txt 1.1 - lines changed: 62, context: html, text, full: html, text
• handle chrom names for chromInfo that are longer than 16 chars
  • src/hg/utils/automation/makeGenomeDb.pl 1.27 - lines changed: 5, context: html, text, full: html, text
• re-run the Panda chain net
  • src/hg/makeDb/doc/mm9.txt 1.122 - lines changed: 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/monDom5.txt 1.18 - lines changed: 9, context: html, text, full: html, text
• initial files from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/marmoset/calJac3/description.html 1.1 - lines changed: 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/gap.html 1.1 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/gold.html 1.1 - lines changed: 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra 1.1 - lines changed: 40, context: html, text, full: html, text
• adding calJac3 to the build
  • src/hg/makeDb/trackDb/makefile 1.283 - lines changed: 1, context: html, text, full: html, text
• have default clade mammal if none found
  • src/hg/hgGateway/hgGateway.c 1.113 - lines changed: 3, context: html, text, full: html, text
• adding marmoset calJac3
  • src/hg/makeDb/genbank/etc/genbank.conf 1.363 - lines changed: 17, context: html, text, full: html, text
• turning ailMel1 back on after reload
  • src/hg/makeDb/genbank/etc/align.dbs 1.110 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.114 - lines changed: 1, context: html, text, full: html, text
• limit custom tracks short label to 128 characters to avoid buffer overflow elsewhere
  • src/hg/lib/customFactory.c 1.116 - lines changed: 2, context: html, text, full: html, text
• do not error out just because the wiki WEB site has disappeared
  • src/hg/lib/wikiTrack.c 1.27 - lines changed: 19, context: html, text, full: html, text