Commits for galt

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

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