Commits for vsmalladi

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

• Added a few mouse cell registrations.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 99, context: html, text, full: html, text
• Fixed DAF for track. Redmine #107.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodePsuRnaSeq.daf - lines changed 14, context: html, text, full: html, text
• Added other terms in DDF for track. Redmine #107.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodePsuRnaSeq.daf - lines changed 2, context: html, text, full: html, text
• Registration of new cell lines and treatments for Gilbert lab.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 102, context: html, text, full: html, text
• First pass of Mouse DAF for FSU Repli-seq. Redmine #6627.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf - lines changed 44, context: html, text, full: html, text
• Merge branch 'Development-Mouse'
• Added MEP cell line for Hardison lab.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 17, context: html, text, full: html, text
• Fixed metadata erore with age and strain for A20, 416B, MEL and mg/ER. Redmine #4469,#4468,#3631.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra - lines changed 108, context: html, text, full: html, text
• Updated strain for ES-CJ7 to be a specific 129 strain.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra - lines changed 7, context: html, text, full: html, text
• Removed out dataed term displayName.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• Removed tissueSourceType otherTerms.html link as the term is not present on the page. Redmine #7100.
  • src/hg/js/utils.js - lines changed 1, context: html, text, full: html, text
• Changed shebang to the correct syntax to be used for python code.
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 1, context: html, text, full: html, text
• Registered HDAC6.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 16, context: html, text, full: html, text
• Fixed spelling of HDAC6 to be consistent with cv.ra.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text
• Added 34 submissions for more processed non-displayed data. Redmine #7089.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 1837, context: html, text, full: html, text
• Added in changes to the DAF.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf - lines changed 25, context: html, text, full: html, text
• Added Ribo-Zero RNA extract type protocol.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Updated DAF for new Signal data.
  • src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf - lines changed 17, context: html, text, full: html, text
• Fixed spelling of organism.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Fixed error in protocol name.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Fixed lab designation for MEP cell type.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Displaying the first 24 experiments from FSU for Mouse. Redmine #6627.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 1105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.ra - lines changed 238, context: html, text, full: html, text
• Added 5 experiments to the track. Redmine #4486.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 79, context: html, text, full: html, text
• Fixed typo's in cv.ra
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Fixed error in meta-data regarding reference to age.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 35, context: html, text, full: html, text
• Added meta-data that was forgotten to be checked in. Redmine #4486.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 580, context: html, text, full: html, text
• Removed comma in Cell's multiple protocols, which is incorrect syntax.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 17, context: html, text, full: html, text
• Commented out T98G protocol that doesn't exist.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 1, context: html, text, full: html, text
• Fixed error in order of tag and term in stanza.
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 2, context: html, text, full: html, text
• Added in approved submissions from beta/cv.ra to public/cv.ra. Redmine #7433.
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 38, context: html, text, full: html, text
• Removed HCT-116 control, which was meant for SYDH Histone track.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 68, context: html, text, full: html, text
• Removed HCT-116 control as this is for the histone track.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra - lines changed 8, context: html, text, full: html, text
• Added trackDescription and metaData variables. Redmine #6627.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html - lines changed 149, context: html, text, full: html, text
• Added 5 new experiments for the track. Redmine #7510.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 577, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra - lines changed 118, context: html, text, full: html, text
• Merge branch 'Development'
• Added 3 submissions for RNA-seq track. Redmine #107.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra - lines changed 450, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra - lines changed 162, context: html, text, full: html, text
• Added 1 submission for release 2 of track. Redmine #7516.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra - lines changed 625, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html - lines changed 263, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra - lines changed 517, context: html, text, full: html, text
• Fixed tag for diffProtD.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Merge branch 'Development-Mouse'
• Fixed issue regarding replicate 1 of an experiment should have been revoked and replicate 2 and 3 should be reclassified as 1 and 2 respectivley. Redmine #5394, Note #63.
  • src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 136, context: html, text, full: html, text
• Added md5sum's for all tracks after the ENCODE Freeze.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 334, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 76, context: html, text, full: html, text
• Added track description for track. Redmine #3631.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html - lines changed 128, context: html, text, full: html, text
• Added md5sum's for files.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 67, context: html, text, full: html, text
• Renamed Alignment files, as there was an error in 2 submissions which had an older daf that didn't require replicates for alignment files. Redmine #4156.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra - lines changed 4, context: html, text, full: html, text
• Fixed some typo's.
  • python/style.txt - lines changed 2, context: html, text, full: html, text
• Fixed typo in metadata surrouding spelling of replicate.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 3, context: html, text, full: html, text
• Removed rel="nofollow" for current tracks being worked on. Redmine #7533.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html - lines changed 166, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.html - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.ra - lines changed 1164, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html - lines changed 222, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html - lines changed 13, context: html, text, full: html, text
• Updated track default and track description. Redmine #6626.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra - lines changed 28, context: html, text, full: html, text
• Fixed matrix link. Redmine#6626.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra - lines changed 1, context: html, text, full: html, text