Commits for wong
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v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260
- removed doEncodeValidate from the testing suite, changed how it worked.
- src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl - lines changed 2409, 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
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 19, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 10, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
- removed non-standard package
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
- this reverts f329d887708f96c02a837be3c02f479c9ad25e81
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 19, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 10, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
- Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81"
This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 19, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 10, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
- changed to GB standard of doing rhe libraries live where you do thing
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 11, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 10, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 12, context: html, text, full: html, text
- added switch for beta and prod assembly choices
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 2, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 3, context: html, text, full: html, text
- src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
- Revert "added switch for beta and prod assembly choices"
This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 2, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 3, context: html, text, full: html, text
- src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
- making things obsolete
- src/hg/encode/encodeValidate/doc/errors.txt - lines changed 21, context: html, text, full: html, text
- src/hg/encode/encodeValidate/obsolete/doc/errors.txt - lines changed 21, context: html, text, full: html, text
- src/hg/encode/encodeValidate/obsolete/tagAlignSanityCheck.pl - lines changed 124, context: html, text, full: html, text
- src/hg/encode/encodeValidate/tagAlignSanityCheck.pl - lines changed 124, context: html, text, full: html, text
- reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeDownloadReadme/redirectTemplateIndex.html - lines changed 31, context: html, text, full: html, text
- src/hg/encode/encodeLoad/makefile - lines changed 15, context: html, text, full: html, text
- src/hg/encode/encodeValidate/config/makefile - lines changed 24, context: html, text, full: html, text
- src/hg/encode/encodeValidate/config/redirectTemplateIndex.html - lines changed 31, context: html, text, full: html, text
- src/hg/encode/encodeValidate/makefile - lines changed 40, context: html, text, full: html, text
- src/hg/utils/automation/makefile - lines changed 22, context: html, text, full: html, text
- removed SafePipe from libraries in unload, it's not being used
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
- removed a random # sign
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 1, context: html, text, full: html, text
- Merge branch 'validate'
- updated usage statement, and renamed variables
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 8, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 7, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 7, context: html, text, full: html, text
- src/hg/utils/automation/Encode.pm - lines changed 6, context: html, text, full: html, text
- removed comment line that is no longer needed
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 9, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 9, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 11, context: html, text, full: html, text
- corrected a mispelling
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 1, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
- resolving merge
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 2, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 16, context: html, text, full: html, text
- src/hg/utils/automation/Encode.pm - lines changed 15, context: html, text, full: html, text
- correct ordering issue
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 1, context: html, text, full: html, text
- fixed a bug
- src/hg/utils/automation/Encode.pm - lines changed 4, context: html, text, full: html, text
- fixed some pre-QA stuff
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 2, context: html, text, full: html, text
- changed the location of the tagging function for the pipeline submissions
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 14, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 4, 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
- src/hg/encode/encodeValidate/doEncodeValidate.pl - 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.
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 5, 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/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
- fixed a mkChangenotes bug, loose was applied to alpha metaDb, but it shouldn't
- python/lib/ucscgenomics/mkChangeNotes.py - lines changed 1, context: html, text, full: html, text
- added bai for skmc
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 1, context: html, text, full: html, text
- updated notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes - lines changed 6, context: html, text, full: html, text
- fixed some bugs QA found
- src/hg/encode/encodeQaInit/encodeQaInit - lines changed 8, context: html, text, full: html, text
- for printing solo report, the gbdb path was set to release path
- python/lib/ucscgenomics/mkChangeNotes.py - lines changed 1, context: html, text, full: html, text
- fixed notes after a mkChange bugfix
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes - lines changed 32, context: html, text, full: html, text
- fleshed out an error message
- src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - 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/wgEncodeUwDgf.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 21, context: html, text, full: html, text
- revoked monocytes cd14 on uw dnase for beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra - lines changed 21, context: html, text, full: html, text
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