Commits for galt

origin/v233_branch to v234_preview (2010-06-07 to 2010-06-15) v234

• v234 preview
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text
• convert to git
  • src/utils/qa/weeklybld/doNewReview.csh - lines changed 4, context: html, text, full: html, text
• Merge branch 'master' of hgwdev:/data/git/kent
• removing test area GBUILDDIR
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• restoring some old test file in non-huge form
  • src/hg/encode/encodeValidate/test/input/genes/known.jan08.gff - lines changed 1000, context: html, text, full: html, text
• restoring some old test file in non-huge form
  • src/hg/encode/encodeValidate/test/input/duke/GM12878_DNase_peaks.bed - lines changed 1000, context: html, text, full: html, text
• adding needed downloads for phastCons6way
  • src/hg/makeDb/doc/danRer6.txt - lines changed 6, context: html, text, full: html, text
• fixing GeneTrack list
  • src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html - lines changed 4, context: html, text, full: html, text
• adding track description page
  • src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html - lines changed 250, context: html, text, full: html, text
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• adding .gitignore to itself at the highest level
  • .gitignore - lines changed 1, context: html, text, full: html, text
• Merge branch 'master' of hgwdev:/data/git/kent
• adding FTP notes
  • src/hg/encode/hgEncodeSubmit/README.FTP - lines changed 17, context: html, text, full: html, text
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty
  • src/hg/utils/automation/Encode.pm - lines changed 0, context: html, text, full: html, text
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 0, context: html, text, full: html, text
  • src/hg/utils/automation/HgDb.pm - lines changed 0, context: html, text, full: html, text
• tweaking git pull to be safer
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/makefile - lines changed 3, context: html, text, full: html, text
• tweaking git pull to be safer, fixing checkbeta target
  • src/hg/htdocs/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 5, context: html, text, full: html, text
• added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push
  • src/utils/qa/weeklybld/buildHgCentralSql.csh - lines changed 9, context: html, text, full: html, text
  • src/utils/qa/weeklybld/updateCgiVersion.csh - lines changed 9, context: html, text, full: html, text
• safer to be agnostic about the git pull for now
  • src/makefile - lines changed 2, 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
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• git convert, rename review to preview as that is more common usage now
  • src/utils/qa/weeklybld/tagPreview.csh - lines changed 30, context: html, text, full: html, text
  • src/utils/qa/weeklybld/tagReview.csh - lines changed 31, context: html, text, full: html, text
• Merge branch 'master' of hgwdev:/data/git/kent
• convert to git
  • src/utils/qa/weeklybld/makeUserApps.csh - lines changed 9, context: html, text, full: html, text
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• moving this to hgdownload repo where it belongs
  • src/hg/htdocs/admin/exe/README.txt - lines changed 17, context: html, text, full: html, text
• convert to git
  • src/utils/qa/weeklybld/tagBeta.csh - lines changed 8, context: html, text, full: html, text
  • src/utils/qa/weeklybld/tagNewBranch.csh - lines changed 10, context: html, text, full: html, text
  • src/utils/qa/weeklybld/updateCgiVersion.csh - lines changed 20, context: html, text, full: html, text
• convert to git
  • src/utils/qa/weeklybld/makeZip.csh - lines changed 31, context: html, text, full: html, text
• convert to git
  • src/utils/qa/weeklybld/doJavaUtilBuild.csh - lines changed 9, context: html, text, full: html, text
• print working dir before exit 1 for additional troubleshooting info
  • src/utils/qa/weeklybld/configureSandbox.csh - lines changed 1, context: html, text, full: html, text
• converting to git
  • src/utils/qa/weeklybld/coBranch.csh - lines changed 5, context: html, text, full: html, text
• conversion of buildUtils.csh to using git
  • src/utils/qa/weeklybld/buildUtils.csh - lines changed 1, context: html, text, full: html, text
• creating BUILDHOME variable
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text
• Merge commit 'origin/master'
• hgcentral.sql is in new hgdownload git build repo
  • src/utils/qa/weeklybld/buildHgCentralSql.csh - lines changed 11, context: html, text, full: html, text
• Merge branch 'master' of galt@hgwdev.cse.ucsc.edu:/data/git/kent
• converted to git using gitFiles the script that checks for CRLF line terminators
  • build/dosEolnCheck - lines changed 5, context: html, text, full: html, text
• conversion to git
  • src/hg/js/makefile - lines changed 3, 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
• adding big test data back smaller
  • src/hg/pslPseudo/tests/input/pseudoEst5MrnaOrf100.psl - lines changed 993, context: html, text, full: html, text
• trying to fix the compiler warnings
  • src/hg/pslPseudo/pslPseudo.c - lines changed 21, context: html, text, full: html, text
• do not want to see .a files either
  • .gitignore - lines changed 1, context: html, text, full: html, text
• restoring some large files that had already become small enough to add back
  • src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.wig - lines changed 10995, context: html, text, full: html, text
  • src/hg/pslMap/tests/input/kgProtMRna.blast - lines changed 2239, context: html, text, full: html, text
  • src/hg/pslMap/tests/input/negQ.chain - lines changed 632, context: html, text, full: html, text
• new location for things under git build - no partial sandbox checkouts available
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, 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
• first quick attempt to change major makefiles from cvs to git.
  • .gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/makefile - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 6, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
  • src/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/qa/makefile - lines changed 2, context: html, text, full: html, text
• renaming .cvsignore files to .gitignore
  • src/blat/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/blat/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/throwback/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/throwback/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/v29skips/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/v29skips/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/autoSql/tests/.cvsignore - lines changed 5, context: html, text, full: html, text
  • src/hg/autoSql/tests/.gitignore - lines changed 5, context: html, text, full: html, text
  • src/hg/checkTableCoords/tests/.cvsignore - lines changed 2, context: html, text, full: html, text
  • src/hg/checkTableCoords/tests/.gitignore - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/.cvsignore - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/.gitignore - lines changed 2, context: html, text, full: html, text
  • src/hg/liftUp/test/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/hg/liftUp/test/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/mafRanges/tests/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/mafRanges/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/test/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/test/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/.cvsignore - lines changed 1, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/.gitignore - lines changed 1, context: html, text, full: html, text
• updates
  • src/utils/qa/weeklybld/buildHgCentralSql.csh - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/weeklybld/makeUserApps.csh - 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 help for pstat2
  • src/parasol/parasol/parasol.c - lines changed 3, 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
• added info about jobtree pstat2 and parahub results fileSize checks
  • src/parasol/version.doc - lines changed 6, context: html, text, full: html, text
• next version increment
  • src/parasol/inc/paraVersion.h - lines changed 1, context: html, text, full: html, text
• handle -1 fileSize means does not exist so skip output
  • src/parasol/paraHub/paraHub.c - lines changed 5, context: html, text, full: html, text
• allowing pstat2 command to optionally use -result=path/results.txt, i.e. for jobTree use
  • src/parasol/parasol/parasol.c - lines changed 11, 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
• not needed
  • src/hg/makeDb/doc/danRer6.txt - lines changed 3, context: html, text, full: html, text
• oops
  • src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra - 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
• changing qateam to encodeteam
  • src/hg/encode/hgEncodeSubmit/runforever.sample - lines changed 2, context: html, text, full: html, text