Commits for wong

v259_preview2 to v259_base (2011-11-01 to 2011-11-07) v259

• made with v2 mkchangenotes
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaChipSeq.release3.notes - lines changed 628, context: html, text, full: html, text
• took out conditional that leaked in for a one time use change
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 3, context: html, text, full: html, text
• removed experiments for which we don't have controls, pushing to next release
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 266, context: html, text, full: html, text
• added in missing controls, took out experiment for which we didn't have a control
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 136, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 48, context: html, text, full: html, text
• updated notes files for the Uw tracks
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes - lines changed 3133, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes - lines changed 2252, context: html, text, full: html, text
• added expId's and dcc's where available
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 17, context: html, text, full: html, text
• added in expIds and dcc accessions
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 81, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 31, context: html, text, full: html, text
• converted internal controlId's to dccAccession
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 1991, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 687, context: html, text, full: html, text
• changed long labels to be more consistent
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 555, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 70, context: html, text, full: html, text
• added md5sums for uw tfbs and histone
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 4, context: html, text, full: html, text
• new notes files for uw tfbs and histone
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes - lines changed 2079, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes - lines changed 1451, context: html, text, full: html, text
• added feature to print a slice of the mdb representative of the release directory files
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 14, context: html, text, full: html, text
• added a switch to print the help
  • src/hg/encode/qaUpdateMetadata/qaUpdateMetadata - lines changed 4, context: html, text, full: html, text
• removed the need for labs.ra (grants)
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 22, context: html, text, full: html, text
• removed the need for labs.ra to provide grant info
  • src/hg/utils/automation/Encode.pm - lines changed 20, context: html, text, full: html, text
• made it so that it first checks with trackDb.wgEncode.ra to try and determine an alpha track.ra file
  • python/lib/ucscgenomics/track.py - lines changed 8, context: html, text, full: html, text
• removed labs.ra and pi.ra from being needed by the pipeline
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 17, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 22, context: html, text, full: html, text
• removed labs.ra from module, i think pi.ra was removed earlier
  • src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
• added a message about the removal of labs.ra
  • src/hg/encode/encodeValidate/doEncodeReport.pl - lines changed 3, context: html, text, full: html, text
• changed a line back
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
• removed getGrants
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
• changed lib include line to not be beta
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
• restored some lines for a clean change
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 9, context: html, text, full: html, text
• added a beta make
  • src/hg/encode/encodeDownloadReadme/makefile - lines changed 2, context: html, text, full: html, text
• Revert "restored some lines for a clean change" This reverts commit 2992650196240f7e5d261da6e70e7ad2d4e2b402.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 9, context: html, text, full: html, text
• more reverts
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 17, 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 21, context: html, text, full: html, text
• reverted yet again
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Revert "removed the need for labs.ra (grants)" This reverts commit 322bc1d109abaddbafa18c2d244bca374610a6e5.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 22, context: html, text, full: html, text
• fixed merge
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• Revert "removed getGrants" This reverts commit a512dbcc007cf4bc7c3a5cc6994938a593f688b8.
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 1, context: html, text, full: html, text
• Revert "removed labs.ra from module, i think pi.ra was removed earlier" This reverts commit 2d5bbffc954b7fb2e6cc4a31e497cf36cb7d9f23.
  • src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
• Revert "removed the need for labs.ra to provide grant info" This reverts commit 644b3e99fdead58a36d512cef312fffab4d050de.
  • src/hg/utils/automation/Encode.pm - lines changed 20, context: html, text, full: html, text
• removed the code for pi.ra
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
• removed the need for labs.ra
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 7, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 28, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm - lines changed 21, context: html, text, full: html, text
• changed how encodeValidate and friends uses packages to allow for same directory location of the packages
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 14, context: html, text, full: html, text