Commits for fang

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• add Histone Modifications by to the long label of new submissions, responding to Steve's pont 4 in note 152 and note 155 in #5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 44, context: html, text, full: html, text
• fixing long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 1, context: html, text, full: html, text
• fix order of the tissues
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 1, context: html, text, full: html, text
• fix adult-24wks to 24w to be consistent with others
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 3, context: html, text, full: html, text
• fix age in longLabel
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 4, context: html, text, full: html, text
• fix order in file list
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 137, context: html, text, full: html, text
• remove 1 before adult8wks, as it may have broken the pull down list below the matrix
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 120, context: html, text, full: html, text
• add 1 in front of ADULT8WKS and 2 to ADULT24WKS, update the dimensionAchecked as well
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 128, context: html, text, full: html, text
• fixes according to Steve's comments in 153, #5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html - lines changed 14, context: html, text, full: html, text
• fixed long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 2, context: html, text, full: html, text
• fix methods
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html - lines changed 4, context: html, text, full: html, text
• fixed Steve's comment 10, 11b, 16b in note 165 #5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html - lines changed 1, context: html, text, full: html, text
• make new views proteomGenomics experiments for search on genome database, gencode annotation, modified peptides, bigbed file
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 36, context: html, text, full: html, text
• create new views for proteomGenomics experiments for search results on genome database, genecode annotation, modified peptides, bigbed file format
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 23, context: html, text, full: html, text
• change version number from 2.0 to 3.1
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 1, context: html, text, full: html, text
• change dafVersion from 2.0 to 3.1
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 1, context: html, text, full: html, text
• fixed the default check box, see Steve's point 5,6 in note 157 and Venkat note 168 in ticket 5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 10, context: html, text, full: html, text
• change dafVersion from 3.1 to 3.0 as the former gets an error when upload
  • src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf - lines changed 1, context: html, text, full: html, text
• fixing cell name, age order, see Steve's point 1, 3 in note 152, ticket #5393 which are the same as this track
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 77, context: html, text, full: html, text
• turn input signal off
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 5, context: html, text, full: html, text
• copy the html from LicrHistone which is the same as this track after correction in responding to all the points in Steve's note 153, points 11b, 16b in note 165 in ticket #5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html - lines changed 23, context: html, text, full: html, text
• add TFBS to MEL, BMDM longLabel
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 10, context: html, text, full: html, text
• fixing the greying box problem, see note 169, 173 in #5393
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
• turn whole brain E14.5 off to fix the grey box problem but the lab wants to have whole brain E14.5 displayed by default, this is in conflict
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 4, context: html, text, full: html, text
• turn off the whole brain E14.5 subtrack, missekd earlier
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 1, context: html, text, full: html, text
• Revert "added in enw tracks for licr histone" This reverts commit dcff6d1eccd504083b3c1194c50f1ac5ebb3ca2f.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra - lines changed 362, context: html, text, full: html, text
• Revert "added in new mouse tracls" This reverts commit be633f8017ea8465308013d3db3c016cf20e73fd.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 3121, context: html, text, full: html, text
• change ADULT8WKS to ADLT8W in all the subtracks, add new html file
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html - lines changed 242, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 1756, context: html, text, full: html, text
• change age=ADLT8W to age=ADULT8WKS to update those submissions loaded before ADULT8WKS is changed to ADLT8W
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 428, context: html, text, full: html, text
• change ADULT8WKS to ADLT8W after update mdb of all the subtracks submitted before ADULT8WKS was changed to ADLT8W
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 36, context: html, text, full: html, text
• update those subtracks submitted before ADULT8WKS was changed to ADLT8W
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 1249, context: html, text, full: html, text
• change ADULT8WKS to 1ADLT8W for ordering, update mdb
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 1873, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 147, context: html, text, full: html, text
• change release note 2 to 3, a test
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html - lines changed 1, context: html, text, full: html, text
• add alpha,beta at the end of xxxLicrHistone.release2, add xxxLicrHistone.release3
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• change wrangler from Venkat to Ruihua in comment section
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 1, context: html, text, full: html, text
• add public at the end of xxxLicrHistone.release2.ra and add alpha,beta to xxxLicrHistone.release3.ra
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• please ignore this change if you are reviewing the code for this section, change back to original as I can't access my sandbox, but it is probably a server error, it actually works fine, I'll need to add the change back after this commit
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• add beta,public to the end of xxxLicrHistone.release2 and alpha to the end of xxxLicrHistone.release3
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• add 0 in front of BCELLxxx to force order
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 5, context: html, text, full: html, text
• remove LicrHistone.release3, add alpha,beta,product to the end of LicrHistone.release2
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• add LicrHistone.release3 alpha
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• change the end of LicrHistone.release2 from alpha,beta,product to beta,product
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• clean up long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 40, context: html, text, full: html, text
• clean up long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra - lines changed 40, context: html, text, full: html, text
• add md5sums
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 2, context: html, text, full: html, text
• try to resolve merge conflict
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 38, context: html, text, full: html, text
• creating the notes file
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release2.notes - lines changed 38, context: html, text, full: html, text
• added expId
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 241, context: html, text, full: html, text
• modified release note
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html - lines changed 3, context: html, text, full: html, text
• fixed release note
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html - lines changed 2, context: html, text, full: html, text
• create trackDb and html files for release2
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html - lines changed 147, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra - lines changed 163, context: html, text, full: html, text
• update html reference and release note
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra - lines changed 1, context: html, text, full: html, text
• update with new submissions
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra - lines changed 1023, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra - lines changed 137, context: html, text, full: html, text
• fix short label
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
• create release1 files
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html - lines changed 146, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 91, context: html, text, full: html, text
• update html
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html - lines changed 6, context: html, text, full: html, text
• try to solve merge conflict
• create notes file
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release2.notes - lines changed 28, context: html, text, full: html, text
• update with new submissions (got distracted to work on other things, this msg may not be accurate
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 203, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 45, context: html, text, full: html, text
• added CaltechRnaSeq.release1.ra to include
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
• fixed a typo
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• trying to fix make error (note 29, ticket #4156, add rep=rep1 at the end of subGroups for Aln track of submission id 6081, 6082
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 2, context: html, text, full: html, text
• removed fields with only one value from sortOrder and filedownload list
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 2, context: html, text, full: html, text
• clean up short and long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 16, context: html, text, full: html, text
• clean up long labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 4, context: html, text, full: html, text
• add expId
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 39, context: html, text, full: html, text
• modify labels
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 16, context: html, text, full: html, text
• remove stanza of Placenta adult-8wks Input, as its corresponding tfbs antibody dataset were not submitted
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra - lines changed 9, context: html, text, full: html, text