markd: changes by commit

branch to review (2010-04-06 to 2010-04-13) v229

• fixed library dependency problems
  • src/hg/makeDb/genbank/common.mk 1.27 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/makefile 1.17 - lines changed: 1, context: html, text, full: html, text
• Better handling of rounding when capping width of label area to 1/2 of width of size of image
  • src/hg/hgTracks/simpleTracks.c 1.131 - lines changed: 4, context: html, text, full: html, text
• reload encodeGencodeGeneKnownMar07
  • src/hg/makeDb/doc/encodeHg18.txt 1.33 - lines changed: 12, context: html, text, full: html, text
• Switch GTF output to being true GTF
  • src/hg/hgTables/gffOut.c 1.21 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.190 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.140 - lines changed: 2, context: html, text, full: html, text
• disable chimp
  • src/hg/makeDb/genbank/etc/align.dbs 1.116 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs 1.108 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.120 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/rr.dbs 1.89 - lines changed: 2, context: html, text, full: html, text
• remove hacks to align human as native on chimp
  • src/hg/makeDb/genbank/etc/genbank.conf 1.368 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignCommon.c 1.6 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbBlat 1.70 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c 1.79 - lines changed: 6, context: html, text, full: html, text
• don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
  • src/hg/makeDb/genbank/src/align/gbAlignRun 1.11 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignStep 1.25 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/download/gbDownloadStep 1.16 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbCommon.pm 1.49 - lines changed: 19, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/process/gbProcessStep 1.14 - lines changed: 1, context: html, text, full: html, text
• need /cluster/bin/ for making downloads
  • src/hg/makeDb/genbank/src/copy/gbMakeDownload 1.22 - lines changed: 1, context: html, text, full: html, text
• remove hack to treat human cDNAs and RefSeqs as native chimp
  • src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra 1.42 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGene.html 1.6 - lines changed: 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html 1.1 - lines changed: 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/est.html 1.4 - lines changed: 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/estWithHs.html 1.1 - lines changed: 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html 1.6 - lines changed: 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/intronEstWithHs.html 1.1 - lines changed: 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/mrna.html 1.4 - lines changed: 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/mrnaWithHs.html 1.1 - lines changed: 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/refGene.html 1.5 - lines changed: 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/refGeneWithHs.html 1.1 - lines changed: 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra 1.56 - lines changed: 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html 1.5 - lines changed: 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoMrnaNoHs.html 1.1 - lines changed: 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGene.html 1.7 - lines changed: 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGeneNoHs.html 1.1 - lines changed: 55, context: html, text, full: html, text
• redo chimp genbank to not special case huamn
  • src/hg/makeDb/doc/panTro1.txt 1.9 - lines changed: 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro2.txt 1.19 - lines changed: 12, context: html, text, full: html, text
• disable native panda refgene, since there are none
  • src/hg/makeDb/genbank/etc/genbank.conf 1.369 - lines changed: 1, context: html, text, full: html, text