hiram: changes by commit

branch to review (2009-07-07 to 2009-07-15) v210

• Fixup broken build on Solaris, add SOCKETLIB
  • src/hg/gigAssembler/checkAgpAndFa/makefile 1.9 - lines changed: 1, context: html, text, full: html, text
• Fixup broken build on Solaris
  • src/hg/gigAssembler/checkNt/checkNt.c 1.6 - lines changed: 3, context: html, text, full: html, text
  • src/hg/gigAssembler/checkOut/checkOut.c 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/gigAssembler/checkQa/checkQa.c 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/gigAssembler/gapper/gapper.c 1.4 - lines changed: 9, context: html, text, full: html, text
  • src/hg/gigAssembler/goldToAgp/goldToAgp.c 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/gigAssembler/mendMap/mendMap.c 1.11 - lines changed: 39, context: html, text, full: html, text
• Add SOCKETLIB for Solaris build
  • src/hg/makeDb/outside/allenBrain/allenCollectSeq/makefile 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/makefile 1.12 - lines changed: 1, context: html, text, full: html, text
  • src/hg/mouseStuff/chainAntiRepeat/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
• Should be using MAKE not make in sub-makes
  • src/hg/protein/kgBestMrna/makefile 1.8 - lines changed: 2, context: html, text, full: html, text
• Should be using MAKE, not make in sub-makes
  • src/hg/protein/kgBestMrna2/makefile 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/protein/kgBestRef2/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
• Print track description html page for transRegCodeProbe table
  • src/hg/hgc/regMotif.c 1.21 - lines changed: 4, context: html, text, full: html, text
• Properly fill an empty cell in a table with nbsp
  • src/hg/lib/hVarSubst.c 1.6 - lines changed: 1, context: html, text, full: html, text
• Adding the lastz matrices and chain matrices to details page
  • src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html 1.2 - lines changed: 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.34 - lines changed: 12, context: html, text, full: html, text
• Update date/time for fetch of this data
  • src/hg/makeDb/trackDb/sacCer/sacCer2/sgdGene.html 1.1 - lines changed: 14, context: html, text, full: html, text
• Fixup sgdToName table
  • src/hg/makeDb/doc/sacCer2.txt 1.11 - lines changed: 29, context: html, text, full: html, text
• the ChainNet tracks should be specified by their db name
  • src/hg/makeDb/trackDb/trackDb.ra 1.520 - lines changed: 59, context: html, text, full: html, text
• Fixup the multiple lastz and axtChain matrix displays
  • src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html 1.2 - lines changed: 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html 1.2 - lines changed: 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html 1.2 - lines changed: 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.36 - lines changed: 8, context: html, text, full: html, text
• danRer6 lastz done, phylo tree 4d site prediction done for 46 way, biocyc data obtained
  • src/hg/makeDb/doc/hg19.txt 1.30 - lines changed: 204, context: html, text, full: html, text
• Done with enough tables to get full hgGene click through to work
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes11.csh 1.4 - lines changed: 142, context: html, text, full: html, text
• Initial source used for the past couple of Ensembl updates
  • src/hg/utils/automation/findEnsFtpNames.sh 1.1 - lines changed: 79, context: html, text, full: html, text
• Ensembl human release v55 today, no longer need to go to pre.ensembl for hg19
  • src/hg/lib/ensFace.c 1.12 - lines changed: 5, context: html, text, full: html, text
• Updated with version 55 gene set pointers
  • src/hg/utils/automation/EnsGeneAutomate.pm 1.18 - lines changed: 168, context: html, text, full: html, text
• Adding loxAfr3 to the build
  • src/hg/makeDb/trackDb/makefile 1.271 - lines changed: 1, context: html, text, full: html, text