File Changes for galt

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

• .gitignore
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    adding .gitignore to itself at the highest level
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    do not want to see .a files either
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    first quick attempt to change major makefiles from cvs to git.
• build/dosEolnCheck
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    converted to git using gitFiles the script that checks for CRLF line terminators
• src/blat/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/.gitignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/throwback/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/throwback/.gitignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/v29skips/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/blat/test/v29skips/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/autoSql/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/checkTableCoords/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/checkTableCoords/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/encode/encodeValidate/test/input/chipseq/FoxP2_SL167.align_25.wig
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    restoring some large files that had already become small enough to add back
• src/hg/encode/encodeValidate/test/input/duke/GM12878_DNase_peaks.bed
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    restoring some old test file in non-huge form
• src/hg/encode/encodeValidate/test/input/genes/known.jan08.gff
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    restoring some old test file in non-huge form
• src/hg/encode/hgEncodeSubmit/README.FTP
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    adding FTP notes
• src/hg/encode/hgEncodeSubmit/runforever.sample
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    changing qateam to encodeteam
• src/hg/htdocs/ENCODE/releaseLog.html
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    "Encode release log update"
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    "Encode release log update"
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    "Encode release log update"
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    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
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    "Encode release log update"
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    "Encode release log update"
• src/hg/htdocs/admin/exe/README.txt
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    moving this to hgdownload repo where it belongs
• src/hg/htdocs/goldenPath/releaseLog.html
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    "Release log update"
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    "Release log update"
  • lines changed 15, 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"
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    "Release log update"
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    "Release log update"
• src/hg/htdocs/makefile
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    tweaking git pull to be safer, fixing checkbeta target
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    first quick attempt to change major makefiles from cvs to git.
• src/hg/js/makefile
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    tweaking git pull to be safer
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    conversion to git
• src/hg/lib/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/lib/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/liftUp/test/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/liftUp/test/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/doc/danRer6.txt
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    adding needed downloads for phastCons6way
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    not needed
• src/hg/makeDb/hgTrackDb/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/hgTrackDb/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/trackDb/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/trackDb/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/makeDb/trackDb/makefile
  • lines changed 5, context: html, text, full: html, text
    tweaking git pull to be safer, fixing checkbeta target
  • lines changed 6, context: html, text, full: html, text
    first quick attempt to change major makefiles from cvs to git.
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    fixing GeneTrack list
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    adding track description page
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
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    oops
• src/hg/mouseStuff/mafRanges/tests/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/hg/mouseStuff/mafRanges/tests/.gitignore
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    renaming .cvsignore files to .gitignore
• src/hg/pslMap/tests/input/kgProtMRna.blast
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    restoring some large files that had already become small enough to add back
• src/hg/pslMap/tests/input/negQ.chain
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    restoring some large files that had already become small enough to add back
• src/hg/pslPseudo/pslPseudo.c
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    trying to fix the compiler warnings
• src/hg/pslPseudo/tests/input/pseudoEst5MrnaOrf100.psl
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    adding big test data back smaller
• src/hg/utils/automation/Encode.pm
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    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/EnsGeneAutomate.pm
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    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/HgDb.pm
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    trying to commit these files with 755 perms that they actually have so they dont appear in the sandbox as dirty
• src/inc/common.mk
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    first quick attempt to change major makefiles from cvs to git.
• src/makefile
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    safer to be agnostic about the git pull for now
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    first quick attempt to change major makefiles from cvs to git.
• src/parasol/inc/paraVersion.h
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    next version increment
• src/parasol/paraHub/paraHub.c
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    handle -1 fileSize means does not exist so skip output
• src/parasol/parasol/parasol.c
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    adding help for pstat2
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    allowing pstat2 command to optionally use -result=path/results.txt, i.e. for jobTree use
• src/parasol/version.doc
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    added info about jobtree pstat2 and parahub results fileSize checks
• src/test/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/test/.gitignore
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    renaming .cvsignore files to .gitignore
• src/utils/qa/makefile
  • lines changed 3, context: html, text, full: html, text
    tweaking git pull to be safer
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    first quick attempt to change major makefiles from cvs to git.
• src/utils/qa/weeklybld/buildEnv.csh
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    v234 preview
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    removing test area GBUILDDIR
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    creating BUILDHOME variable
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    new location for things under git build - no partial sandbox checkouts available
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push
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    hgcentral.sql is in new hgdownload git build repo
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    updates
• src/utils/qa/weeklybld/buildUtils.csh
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    conversion of buildUtils.csh to using git
• src/utils/qa/weeklybld/coBranch.csh
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    converting to git
• src/utils/qa/weeklybld/configureSandbox.csh
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    print working dir before exit 1 for additional troubleshooting info
• src/utils/qa/weeklybld/doJavaUtilBuild.csh
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    convert to git
• src/utils/qa/weeklybld/doNewReview.csh
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    convert to git
• src/utils/qa/weeklybld/makeUserApps.csh
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    convert to git
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    updates
• src/utils/qa/weeklybld/makeZip.csh
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    convert to git
• src/utils/qa/weeklybld/tagBeta.csh
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    convert to git
• src/utils/qa/weeklybld/tagNewBranch.csh
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    convert to git
• src/utils/qa/weeklybld/tagPreview.csh
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    git convert, rename review to preview as that is more common usage now
• src/utils/qa/weeklybld/tagReview.csh
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    git convert, rename review to preview as that is more common usage now
• src/utils/qa/weeklybld/updateCgiVersion.csh
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    added check for being on master branch since we should always be there in the build-kent repo, and also added necessary git push
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    convert to git
• src/utils/scaffoldFaToAgp/test/.cvsignore
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    renaming .cvsignore files to .gitignore
• src/utils/scaffoldFaToAgp/test/.gitignore
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    renaming .cvsignore files to .gitignore