Commits for wong

v255_preview2 to v255_base (2011-08-02 to 2011-08-08) v255

• cleaned up code, rewrote other parts, added function to check group write permissions before trying to create file
  • src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl - lines changed 58, context: html, text, full: html, text
• added track displays and conventions
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html - lines changed 8, context: html, text, full: html, text
• added tag to show that a label was autogenerated
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
• removed downloadstemplate from encodevalidate/config directory
  • src/hg/encode/encodeValidate/config/downloadsReadmeTemplate.txt - lines changed 45, context: html, text, full: html, text
• corrected files.txt line and removed line referencing md5sum
  • src/hg/encode/encodeDownloadReadme/downloadsReadmeTemplate.txt - lines changed 3, context: html, text, full: html, text
• added in first version of encodeMkFilesList
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 513, context: html, text, full: html, text
  • src/hg/encode/encodeMkFilesList/makefile - lines changed 27, context: html, text, full: html, text
• fixed a bug when using a different directory, and when the md5sum.history file is broken
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 19, context: html, text, full: html, text
• added notes for sydh tfbs and uw 5c
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 3911, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUw5C.release1.notes - lines changed 84, context: html, text, full: html, text
• repleace index.html with README.txt
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 1, context: html, text, full: html, text
• updated sydhtfbs and uw5c notes files
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 5166, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUw5C.release1.notes - lines changed 5, context: html, text, full: html, text
• made metadata file for gencode v3
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 153, context: html, text, full: html, text
• removed quotes
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 4, context: html, text, full: html, text
• added gencode to makefile
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• this is my hand made one
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 115, context: html, text, full: html, text
• reprinted out again
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 26, context: html, text, full: html, text
• put reminder to email
  • src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl - lines changed 1, context: html, text, full: html, text
• added functionality to check for README.txt and if not there, put it in.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 36, context: html, text, full: html, text
• comment out metadata lines
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra - lines changed 3, context: html, text, full: html, text