Commits for cricket

v264_base to v265_preview (2012-03-06 to 2012-03-13) v265

• Swapped grant and lab
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 3, context: html, text, full: html, text
• Removing metaData from rn4
  • src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Changing the track name to the table name since no other composite is using this table, see ticket 7083
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra - lines changed 2, context: html, text, full: html, text
• Added many cell lines and tried to get the labels looking good
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 5054, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 3713, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 885, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra - lines changed 865, context: html, text, full: html, text
• Adding the new metaData for sub 5768 which replaced 5120
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 51, context: html, text, full: html, text
• Changing the track name to the table name to deal with the issue in ticket 7222
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
• Changing for H3K4Me3 according to ticket #7222
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra - lines changed 2, context: html, text, full: html, text
• V4 has been replaced by V11
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV4.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV4.ra - lines changed 24, context: html, text, full: html, text
• Using git to track proposed changes to validateFiles usage statement
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Using git to track proposed changes to validateFiles usage statement
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 59, context: html, text, full: html, text
• First I think we should change the beginning part to all be the same tense and to be the completion of the sentance validateFiles does ...
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 9, context: html, text, full: html, text
• Changing the type to have consistent formatting, the links need to be double checked
  • src/hg/encode/validateFiles/validateFilesUsage - lines changed 13, context: html, text, full: html, text
• Removing metaDb from panTro2
  • src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Removing metaDb from panTro2
  • src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Removing metaData from canFam2
  • src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Removing metaData on bosTau4
  • src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Removing the metaDb line from trackDb
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra - lines changed 1, context: html, text, full: html, text
• alphabetizing
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 8, context: html, text, full: html, text
• Adding composite line in the metaDb to hopefully be able to make on beta
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeNhgriBip.ra - lines changed 1, context: html, text, full: html, text
• Adding a lot of data for Short and Long, fixing up the labels and the metaData
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 2495, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 162, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 605, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra - lines changed 896, context: html, text, full: html, text
• Trying to add magic number to see if that helps beta
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeNhgriBip.ra - lines changed 4, context: html, text, full: html, text
• Fixing the merge
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 1736, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 6, context: html, text, full: html, text
• Adding merged cell types, this is likely to cause a merge conflict with Willy's cv changes
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 280, context: html, text, full: html, text
• Willy's changes to the urls and terms
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 373, context: html, text, full: html, text
• Adding changes the Willy did to merge the donor cell types into one
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 317, context: html, text, full: html, text
• Fixing up NHGRI Bip hg18 metaData
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra - lines changed 2, context: html, text, full: html, text
• This is my first draft at making a TFBSValid track, it is not a functional track but a place holder
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassTfbsValid.html - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassTfbsValid.ra - lines changed 11, context: html, text, full: html, text
• Adding donorId
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 15, context: html, text, full: html, text
• Adding notes file that is compared to release1
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrRnaSeq.release2.notes - lines changed 418, context: html, text, full: html, text