File Changes for wong

v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 1, context: html, text, full: html, text
    fixed a mkChangenotes bug, loose was applied to alpha metaDb, but it shouldn't
  • lines changed 1, context: html, text, full: html, text
    for printing solo report, the gbdb path was set to release path
• src/hg/encode/encodeDownloadReadme/redirectTemplateIndex.html
  • lines changed 31, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 19, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
  • lines changed 19, context: html, text, full: html, text
    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
  • lines changed 19, context: html, text, full: html, text
    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 11, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
  • lines changed 2, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 2, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 8, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 9, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
  • lines changed 2, context: html, text, full: html, text
    resolving merge
  • lines changed 14, context: html, text, full: html, text
    changed the location of the tagging function for the pipeline submissions
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 10, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
  • lines changed 10, context: html, text, full: html, text
    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
  • lines changed 10, context: html, text, full: html, text
    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 10, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
  • lines changed 1, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 1, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 1, context: html, text, full: html, text
    removed SafePipe from libraries in unload, it's not being used
  • lines changed 7, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 9, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
  • lines changed 16, context: html, text, full: html, text
    resolving merge
• src/hg/encode/encodeLoad/makefile
  • lines changed 15, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 8, context: html, text, full: html, text
    fixed some bugs QA found
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 7, context: html, text, full: html, text
    fleshed out an error message
• src/hg/encode/encodeValidate/config/makefile
  • lines changed 24, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/config/redirectTemplateIndex.html
  • lines changed 31, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 12, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
  • lines changed 1, context: html, text, full: html, text
    removed non-standard package
  • lines changed 12, context: html, text, full: html, text
    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
  • lines changed 12, context: html, text, full: html, text
    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 12, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
  • lines changed 3, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 3, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 7, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 11, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
  • lines changed 4, context: html, text, full: html, text
    changed the location of the tagging function for the pipeline submissions
  • lines changed 5, context: html, text, full: html, text
    put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate
  • lines changed 5, context: html, text, full: html, text
    Revert "put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate" This reverts commit dadaf46d634bad2f66b8391d7567f58de974fc26.
  • lines changed 2, context: html, text, full: html, text
    redid how the previous commit handled things, it turns out at that point in the code, validate has chdired into the submit directory
• src/hg/encode/encodeValidate/doc/errors.txt
  • lines changed 21, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/makefile
  • lines changed 40, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
  • lines changed 2409, context: html, text, full: html, text
    removed doEncodeValidate from the testing suite, changed how it worked.
• src/hg/encode/encodeValidate/obsolete/doc/errors.txt
  • lines changed 21, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/obsolete/tagAlignSanityCheck.pl
  • lines changed 124, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/tagAlignSanityCheck.pl
  • lines changed 124, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/makefile
  • lines changed 3, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
  • lines changed 6, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
  • lines changed 32, context: html, text, full: html, text
    fixed notes after a mkChange bugfix
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    removed a random # sign
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 7, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 6, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    added bai for skmc
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 5, context: html, text, full: html, text
    revoked monocytes cd14 on uw dnase for beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 36, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 21, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 21, context: html, text, full: html, text
    revoked monocytes cd14 on uw dnase for beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    correct ordering issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 1, context: html, text, full: html, text
    fixed some pre-QA stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 2, context: html, text, full: html, text
    fixed some pre-QA stuff
• src/hg/utils/automation/Encode.pm
  • lines changed 13, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 13, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 6, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 15, context: html, text, full: html, text
    resolving merge
  • lines changed 4, context: html, text, full: html, text
    fixed a bug
• src/hg/utils/automation/makefile
  • lines changed 22, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/inc/common.mk
  • lines changed 10, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline