hiram: changes by file

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

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