Commits for hiram

v275_preview to v275_preview2 (2012-10-16 to 2012-10-23) v275

• adding petMar2 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding petMar2 Lamprey redmine 9153
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• adding cerSim1 and petMar2 completely clean
  • src/hg/makeDb/schema/all.joiner - lines changed 31, context: html, text, full: html, text
• petMar2 liftOver constructed and blanks at ends of lines removed
  • src/hg/makeDb/doc/petMar1.txt - lines changed 19, context: html, text, full: html, text
• standardize usage message to place into the build
  • src/utils/faRandomize/faRandomize.c - lines changed 8, context: html, text, full: html, text
  • src/utils/faRandomize/makefile - lines changed 3, context: html, text, full: html, text
• adding faRandomize to the build
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• adding paraSync to the build
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• adding bedExtendRanges and makeTableList to the build
  • src/hg/utils/bedExtendRanges/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text
• adding petMar2
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• add note about dlopen routines in library -ldl
  • src/product/README.building.source - lines changed 12, context: html, text, full: html, text
• rearrange -lm to be after mysqllibs redmine 9101
  • src/hg/geneBounds/estLibStats/makefile - lines changed 1, context: html, text, full: html, text
• adding recent new assemblies, rhino, chinchilla, lamprey
  • src/hg/utils/automation/configFiles/cerSim1.config.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/automation/configFiles/chiLan1.config.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/automation/configFiles/petMar2.config.ra - lines changed 23, context: html, text, full: html, text
• adding Lancelet v2.0 braFlo2 to the build
  • src/hg/makeDb/trackDb/lancelet/braFlo2/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/braFlo2/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/braFlo2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/braFlo2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• starting new Lancelet assembly v2.0
  • src/hg/makeDb/doc/braFlo2.txt - lines changed 418, context: html, text, full: html, text
• resolve GIT conflict
  • src/hg/makeDb/doc/petMar2.txt - lines changed 194, context: html, text, full: html, text
• adding additional Lancelet names for Branchiostoma
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
• adding braFlo2 - Lancelet - Branchiostoma floridae
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• running genbank
  • src/hg/makeDb/doc/braFlo2.txt - lines changed 82, context: html, text, full: html, text
• adding hgGcPercent to the userApps delivery
  • src/hg/makeDb/hgGcPercent/makefile - lines changed 8, context: html, text, full: html, text
  • src/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 1, context: html, text, full: html, text
• Added braFlo2.
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• done with genbank alignments
  • src/hg/makeDb/doc/braFlo2.txt - lines changed 46, context: html, text, full: html, text
• renaming primatesChainNet to euarchontoglireChainNet
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra - lines changed 242, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra - lines changed 226, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text
• drBlastTab reload for danRer7 Ensembl update
  • src/hg/makeDb/doc/blastTab.txt - lines changed 399, context: html, text, full: html, text
• adding cytoband tables for Chromosome Band track
  • src/hg/makeDb/doc/mm10.txt - lines changed 29, context: html, text, full: html, text
• update to handle mm10 correctly
  • src/utils/ncbi/createNcbiCytoBand.pl - lines changed 3, context: html, text, full: html, text
  • src/utils/ncbi/cytoBandVerify.pl - lines changed 1, context: html, text, full: html, text
• trying to get a unique RM library from Robert Hubley
  • src/hg/makeDb/doc/allMis1.txt - lines changed 367, context: html, text, full: html, text
• ready for default position and pushQ entry
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 7, context: html, text, full: html, text
• running lastz for petMar2 and cerSim1
  • src/hg/makeDb/doc/hg19.txt - lines changed 137, context: html, text, full: html, text
• do not need to check refLink with kgProtAlias on dm3
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• override for quality table maximum limit
  • src/hg/makeDb/trackDb/lizard/anoCar1/trackDb.ra - lines changed 2, context: html, text, full: html, text
• corrected ncbiAssemblyId
  • src/hg/utils/automation/configFiles/rn5.config.ra - lines changed 1, context: html, text, full: html, text
• better generic location for these ideogram files
  • src/hg/makeDb/doc/mm10.txt - lines changed 6, context: html, text, full: html, text
• lastz Lamprey <-> Lancelet
  • src/hg/makeDb/doc/braFlo2.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar2.txt - lines changed 46, context: html, text, full: html, text