File Changes for galt

v235_base to v236_preview (2010-07-06 to 2010-07-13) v236

• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • lines changed 1, context: html, text, full: html, text
    making the ftp list be sorted as requested
  • lines changed 25, context: html, text, full: html, text
    add paraFetchStatus monitoring
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 3, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
  • lines changed 24, context: html, text, full: html, text
    convert to using paraFetch instead of wget, fix to allow for mixed-case extension, added function for displaying greek disk-size suffixes for human-friendly display
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 6, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 2, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 5, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
• src/hg/makeDb/doc/hg18.txt
  • lines changed 16, context: html, text, full: html, text
    adding DARNED the DAtabase of RNa EDiting
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 22, context: html, text, full: html, text
    darned - the database of rna-editing
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    darned - the database of rna-editing
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 11, context: html, text, full: html, text
    little bit more cleanup on danRer6 conservation descr page
  • lines changed 218, context: html, text, full: html, text
    re-doing danRer6 description page using hg19.cons46way.html as the model
• src/hg/near/hgNear/hgNearData/kegg.html
  • lines changed 1, context: html, text, full: html, text
    typo
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    oops 64 bit has precedence
  • lines changed 5, context: html, text, full: html, text
    oops support for PNG path for 32-bit systems
  • lines changed 48, context: html, text, full: html, text
    trying to autodetect PNG,SSL,BAM; also trying to use PNG statically linked
  • lines changed 2, context: html, text, full: html, text
    cannot yet have png libraries dependency required for default build
• src/inc/net.h
  • lines changed 1, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    remove unneeded flush
  • lines changed 1, context: html, text, full: html, text
    oops, only need to re-open unfinished parts
  • lines changed 30, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    added paraFetch
• src/utils/paraFetch/paraFetch.c
  • lines changed 6, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v236 preview
  • lines changed 4, context: html, text, full: html, text
    try removing the USE_X settings, should not need them now that autodection is in
  • lines changed 1, context: html, text, full: html, text
    adding PNG
• src/utils/qa/weeklybld/buildUtils.csh
  • lines changed 1, context: html, text, full: html, text
    oops backwards
• src/utils/qa/weeklybld/cherryPickCommits.csh
  • lines changed 2, context: html, text, full: html, text
    more tweaks to cherry-picking
  • lines changed 9, context: html, text, full: html, text
    more fixes and tweaks
  • lines changed 3, context: html, text, full: html, text
    include more detail in the notification about the cherry-picked commit
  • lines changed 4, context: html, text, full: html, text
    sometimes the working dirs do not exist yet when cherrypicking
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 4, context: html, text, full: html, text
    oops need to change $dir to $branch throughout
• src/utils/qa/weeklybld/defaultBuildSettings.mk
  • lines changed 1, context: html, text, full: html, text
    adding switch for PNG libraries dependency
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 2, context: html, text, full: html, text
    convert to git
  • lines changed 2, context: html, text, full: html, text
    more convert to git doNewBranch.csh
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • lines changed 3, context: html, text, full: html, text
    static things do not need to be turned off for downloadable utils build
  • lines changed 1, context: html, text, full: html, text
    adding switch for PNG libraries dependency
• src/utils/twoBitInfo/twoBitInfo.c
  • lines changed 3, context: html, text, full: html, text
    fixing help message for twoBitInfo