All File Changes

v243_preview2 to v243_base (2010-10-26 to 2010-11-02) v243

• src/ameme/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing hardcoded -lpg from L because it breaks the build on systemsthat don't have libpng. inc/common.mk does some wildcard matching to find the appropriate lib for png if it exists.
• src/hg/encode/DAFs/2.0/sunyRnaSeq.daf
  • lines changed 55, context: html, text, full: html, text
    trying to develop new daf with SUNY, these are trials
• src/hg/encode/DAFs/2.0/sunySwitchgear.daf
  • lines changed 26, context: html, text, full: html, text
    trying to develop new daf with SUNY, these are trials
• src/hg/encode/DAFs/2.0/sunyTiling.daf
  • lines changed 6, context: html, text, full: html, text
    updated the DAF to currently used one
• src/hg/encode/docId/docIdSubmitDir/makefile
  • lines changed 1, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/docIdTidy/docIdTidy.c
  • lines changed 153, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/docIdTidy/makefile
  • lines changed 19, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/inc/docId.h
  • lines changed 5, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/lib/docIdSub.as
  • lines changed 2, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/lib/docIdSub.c
  • lines changed 52, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/docId/lib/docIdSub.sql
  • lines changed 6, context: html, text, full: html, text
    added tidy program to compress and generated md5sums (and do reports?) added some new fields to the docIdSub table.
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 1, context: html, text, full: html, text
    as per my code review, I have changed coding style to remove quotes
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 4, context: html, text, full: html, text
    Loader should not fail on preexisting files. That is the validator's job.
  • lines changed 4, context: html, text, full: html, text
    Oops, missed one.
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 35, context: html, text, full: html, text
    Updated validation document nameing, so that links to documents would work. Also sperated two antibodies out
  • lines changed 1, context: html, text, full: html, text
    Updated validation document nameing, so that links to documents would work. Also sperated two antibodies for target YY1
  • lines changed 101, context: html, text, full: html, text
    Added 5 new cell lines, on new SOP and 3 new treatments for Crawford
  • lines changed 20, context: html, text, full: html, text
    Minor corrections to Crawfords most recent cells and treatments
  • lines changed 12, context: html, text, full: html, text
    Updated target lables for antibodies, addressing issue 1545
  • lines changed 18, context: html, text, full: html, text
    Added HA-sp human cell type
  • lines changed 443, context: html, text, full: html, text
    Added typeOfTerm category to allow defining controlled vocabulary and other metadata terms in one place. Putting this in the cv.ra keeps it coordinated with the cv. This will probably be used by hgEncodeVocab to display term definitions. It should be used by Track Search for the white list of searchble terms and '...' metadata to distinguish linkable terms.
  • lines changed 36, context: html, text, full: html, text
    beginning the merge of Tim and Cricket's changes to typOfTerm
  • lines changed 7544, context: html, text, full: html, text
    this file has moved to kent/src/hg/makeDb/trackDb/cv/alpha/cv.ra
• src/hg/encode/encodeValidate/makefile
  • lines changed 19, context: html, text, full: html, text
    move to a release controlled cv.ra #1474ENCODE submission pipeline now uses *alpha* version of cv.ra which is how it has been. Maybe it should use beta or public??
  • lines changed 3, context: html, text, full: html, text
    oops.. targets weren't quite right. Now cv.ra gets installed in the right places
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • lines changed 1, context: html, text, full: html, text
    needs @, this variable is set by the re-factored get_ftp_list
  • lines changed 12, context: html, text, full: html, text
    adding download links for ddf and daf as requested by Kate
  • lines changed 2, context: html, text, full: html, text
    this variable needs at-sign too
  • lines changed 4, context: html, text, full: html, text
    ask user what they want to do with the download by setting content-disposition header
  • lines changed 10, context: html, text, full: html, text
    preserving the specific daf or ddf filename
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show_daf.rhtml
  • lines changed 1, context: html, text, full: html, text
    adding download links for ddf and daf as requested by Kate
  • lines changed 1, context: html, text, full: html, text
    preserving the specific daf or ddf filename
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show_ddf.rhtml
  • lines changed 1, context: html, text, full: html, text
    adding download links for ddf and daf as requested by Kate
  • lines changed 1, context: html, text, full: html, text
    preserving the specific daf or ddf filename
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 3, context: html, text, full: html, text
    preserving the specific daf or ddf filename
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 490, context: html, text, full: html, text
    Added support for getting antibodies by target. Added support for 'label' as the last field. Added support for labs and dataTypes
  • lines changed 13, context: html, text, full: html, text
    Kate wants antibody as first column of table even though sort is by target, then antibidy
• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    Oops, forgot desc when ordering by dbDb.name.
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    Uncommenting/adding links for new track types bedDetail and pgSnp.
  • lines changed 4, context: html, text, full: html, text
    Whoops, forgot to add links (and commas) in both places in last commit.
• src/hg/hgTables/gffOut.c
  • lines changed 12, context: html, text, full: html, text
    Code Review #1452 (v243 preview1): comment additions & clarificationsrequested by Melissa.
• src/hg/hgTracks/cds.c
  • lines changed 3, context: html, text, full: html, text
    Code Review #1519 (v243 preview2): Adding comment to explain use ofmod-6 for alternating codons, thanks Melissa.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Reusable blueLines bg image must distinguish reverse complement, and insideX doesn't do that for some strange reason.
• src/hg/hgTracks/searchTracks.c
  • lines changed 85, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    can now do map contigs with a custom URL if present in trackDb
  • lines changed 5, context: html, text, full: html, text
    allow for no URL in a ctgPos click
• src/hg/hgc/wiggleClick.c
  • lines changed 1, context: html, text, full: html, text
    Fix for #1190: if no data was in range, and there wasn't a max range to view set, then the code would errnoneously put out a message about zooming into a window with fewer than 0 bases. Now it correctly says there is no data in the range if there is no data in range
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 70, context: html, text, full: html, text
    Changed links in the bedDetail section, and changed pgSnp section so that it matches other sections that explain how to make a custom track.
• src/hg/htdocs/cite.html
  • lines changed 8, context: html, text, full: html, text
    Added updated refs for new NAR paper.
  • lines changed 1, context: html, text, full: html, text
    For to italicize journal name.
• src/hg/htdocs/goldenPath/help/trackSearch.html
  • lines changed 4, context: html, text, full: html, text
    Redmine #936, note 20: made Mary's suggestions to the Track Search help doc
  • lines changed 46, context: html, text, full: html, text
    updated code to xhtml 1.0 standards for the most part
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 8, context: html, text, full: html, text
    Added updated refs for new NAR paper.
  • lines changed 1, context: html, text, full: html, text
    For to italicize journal name.
• src/hg/htdocs/makefile
  • lines changed 11, context: html, text, full: html, text
    Bug #1211 (hg/makefile does not descend into hg/htdocs/): Added htdocsto hg/makefile's BROWSER_BINS, like js, so that all of the targets that use BROWSER_BINS descend into htdocs. Unlike js/makefile, htdocs/makefile does not create the -${USER} directory if it doesn't exist, because Apache config change is required (and permissions for apache/) -- cluster-admin need to handle that. Instead, htdocs' user target checks for the existence of ${DOCUMENTROOT}-${USER} first.
• src/hg/htdocs/style/makefile
  • lines changed 3, context: html, text, full: html, text
    Bug #1211 (hg/makefile does not descend into hg/htdocs/):htdocs/style/makefile also needs to test for existence of -$USER.
• src/hg/inc/mdb.h
  • lines changed 3, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v243
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    Links to controlled vocabulary for antibodies will now use target to get set of antibodies
  • lines changed 170, context: html, text, full: html, text
    Fixed problem with bam views. This fix extended to psl and genePred views which would also have had problems. This code also cleans up bam cfg spacing and adds links to selected cv.ra terms found in the '...' metadata table
• src/hg/lib/mdb.c
  • lines changed 91, context: html, text, full: html, text
    Moved mdb/cv terms white list to mdb library code. Now it can be used both by trackSearch and by metadata '...' table which will have links for select terms to hgEncodeVocab.
  • lines changed 2, context: html, text, full: html, text
    Fixed sizing of whiteList array
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 21, context: html, text, full: html, text
    add bacEnd track contruction procedure
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 235, context: html, text, full: html, text
    Wrangling to get round 2 of Broad's hg19 submissions. Peaks are still missing
• src/hg/makeDb/doc/hg18.txt
  • lines changed 8, context: html, text, full: html, text
    Monthly update of GWAS Catalog track in hg18 & hg19.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Monthly update of GWAS Catalog track in hg18 & hg19.
• src/hg/makeDb/doc/melHap1.txt
  • lines changed 1, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 2, context: html, text, full: html, text
    Fixed help typos
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    redmine #271 all.joiner error fixed
  • lines changed 4, context: html, text, full: html, text
    added bacEnds and bacEndCalJac3Singles to tablesIgnored per Hiram
  • lines changed 7, context: html, text, full: html, text
    reamine bug #271 fix
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 7527, context: html, text, full: html, text
    move to a release controlled cv.ra #1474ENCODE submission pipeline now uses *alpha* version of cv.ra which is how it has been. Maybe it should use beta or public??
  • lines changed 36, context: html, text, full: html, text
    update to newest version. This checkin will be followed by removing cv.ra from ~/kent/src/hg/encode/encodeValidate/config
  • lines changed 40, context: html, text, full: html, text
    Added PrEC, 8988T, and HTR8svn
  • lines changed 16, context: html, text, full: html, text
    Removed an entry for Trophobl, which has been superseded by HTR8svn
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 7527, context: html, text, full: html, text
    move to a release controlled cv.ra #1474ENCODE submission pipeline now uses *alpha* version of cv.ra which is how it has been. Maybe it should use beta or public??
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 7527, context: html, text, full: html, text
    move to a release controlled cv.ra #1474ENCODE submission pipeline now uses *alpha* version of cv.ra which is how it has been. Maybe it should use beta or public??
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 129, context: html, text, full: html, text
    Initial descriptions for nomLeu1.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    Initial descriptions for nomLeu1.
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 22, context: html, text, full: html, text
    Added a bit more detail
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 121, context: html, text, full: html, text
    bug1301#15, there were missing entries in this metaDb. They are now present.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    pushing out some metaDb changes for ENCODE CSHL Long RNA-seq
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 460, context: html, text, full: html, text
    pushing out some metaDb changes for ENCODE CSHL Long RNA-seq
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisPet.ra
  • lines changed 121, context: html, text, full: html, text
    pushing out some metaDb changes for wgEncodeGisDna.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    pushing out some metaDb changes for ENCODE CSHL Long RNA-seq
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 460, context: html, text, full: html, text
    pushing out some metaDb changes for ENCODE CSHL Long RNA-seq
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisPet.ra
  • lines changed 121, context: html, text, full: html, text
    pushing out some metaDb changes for wgEncodeGisDna.ra
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added hyphen to protein-coding when used as adjective
  • lines changed 2, context: html, text, full: html, text
    some cactus stuff for Benedict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Updated metadata for new UW TFBS track. Not complete need to improve
  • lines changed 1, context: html, text, full: html, text
    Updated trackDb and metadata make file.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 2042, context: html, text, full: html, text
    40 resubmissions added/changed a lot of metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2071, context: html, text, full: html, text
    15 new submissions added
  • lines changed 96, context: html, text, full: html, text
    added hg18 fastqs/fastas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 477, context: html, text, full: html, text
    added hg18 fastqs/fastas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 970, context: html, text, full: html, text
    Displayed 9 submissions for UTA chip Seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 157, context: html, text, full: html, text
    Added submission 2515
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 71, context: html, text, full: html, text
    Updated metaData for Uwtfbs and Histone for inputType to controlId split.
  • lines changed 8034, context: html, text, full: html, text
    updated UW Histone track with 67 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 1295, context: html, text, full: html, text
    Updated metadata for new UW TFBS track. Not complete need to improve
  • lines changed 53, context: html, text, full: html, text
    Updated metaData for Uwtfbs and Histone for inputType to controlId split.
  • lines changed 4, context: html, text, full: html, text
    Cleaned up inputType from metaDb
  • lines changed 4541, context: html, text, full: html, text
    Preliminary metadata for UW TFBS data.
  • lines changed 733, context: html, text, full: html, text
    Split CTCF and Input data for UW TFBS data from all Uw Histone data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 101, context: html, text, full: html, text
    added the fastqs from hg18 to the metaDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    the ctgPos2 Supercontig is better called GRC Map Contigs
  • lines changed 2, context: html, text, full: html, text
    turn off external URL for GRC ctgPos2
  • lines changed 1, context: html, text, full: html, text
    added hyphen to protein-coding when used as adjective
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Split TFBS and Histone data for UW. This is a trial and not the entire deal
  • lines changed 2, context: html, text, full: html, text
    :Left in line from resolving merge conflict
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
  • lines changed 1, context: html, text, full: html, text
    added hyphen to protein-coding when used as adjective
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 916, context: html, text, full: html, text
    15 new submissions added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    purple is more than 2 locations
  • lines changed 5, context: html, text, full: html, text
    minor edits such as encoding an email address, changing 1 to one, changing a few sentences to past tense for consistency, fixing a couple typos
  • lines changed 5, context: html, text, full: html, text
    fixed a few more typos
  • lines changed 2, context: html, text, full: html, text
    adding SAM & bowtie links so users can easily find further info, adding information about why the Mappying Quality and sequence quality scores are the same for all records, clarifying the the methods section that the quality score displayed as 40 is the sequence quality score (since there are two quality scores)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 105, context: html, text, full: html, text
    changed long labels, short labels and matrix labels per Kate request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra
  • lines changed 302, context: html, text, full: html, text
    Trying to work on filter composite option
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 302, context: html, text, full: html, text
    Displayed 9 submissions for UTA chip Seq
  • lines changed 1, context: html, text, full: html, text
    Added correct term for Estrogen treatment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 28, context: html, text, full: html, text
    Added submission 2515
  • lines changed 3, context: html, text, full: html, text
    Added treatment for Gliobla cells
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 45, context: html, text, full: html, text
    changing labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 337, context: html, text, full: html, text
    Updated the track configuration to display replicate
  • lines changed 2, context: html, text, full: html, text
    Updated typo's when trying to display replicate
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 1415, context: html, text, full: html, text
    Split TFBS and Histone data for UW. This is a trial and not the entire deal
  • lines changed 163, context: html, text, full: html, text
    Removed CTCF tacks that were added during the merge
  • lines changed 4, context: html, text, full: html, text
    Updated the track configuration to display replicate
  • lines changed 2, context: html, text, full: html, text
    Updated typo's when trying to display replicate
  • lines changed 1, context: html, text, full: html, text
    Oops. Fixed accidentl delete
  • lines changed 1571, context: html, text, full: html, text
    updated UW Histone track with 67 submissions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 1652, context: html, text, full: html, text
    Split TFBS and Histone data for UW. This is a trial and not the entire deal
  • lines changed 1, context: html, text, full: html, text
    Updated the Track long label to include Sites
  • lines changed 11, context: html, text, full: html, text
    Updated trackDb and metadata make file.
  • lines changed 18, context: html, text, full: html, text
    Updated trackDb error for referencing other tables of input
  • lines changed 307, context: html, text, full: html, text
    Removed all mentioned of rank from metaData,long labels
  • lines changed 2, context: html, text, full: html, text
    Updated the track configuration to display replicate
  • lines changed 166, context: html, text, full: html, text
    Split CTCF and Input data for UW TFBS data from all Uw Histone data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html
  • lines changed 65, context: html, text, full: html, text
    Updated track description with one provided by lab
• src/hg/makeDb/trackDb/makefile
  • lines changed 6, context: html, text, full: html, text
    move to a release controlled cv.ra #1474ENCODE submission pipeline now uses *alpha* version of cv.ra which is how it has been. Maybe it should use beta or public??
  • lines changed 1, context: html, text, full: html, text
    Added nomLeu1 to DBS.
  • lines changed 4, context: html, text, full: html, text
    make sure that the makeTrackIndex is using the right trackDb
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed short label for bacEndSingles because it was one character too long
• src/hg/makeDb/trackDb/worm/bruMal1/description.html
  • lines changed 51, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/trackDb/worm/bruMal1/gold.html
  • lines changed 22, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/trackDb/worm/bruMal1/trackDb.ra
  • lines changed 60, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/trackDb/worm/melHap1/description.html
  • lines changed 44, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/trackDb/worm/melHap1/gold.html
  • lines changed 4, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makeDb/trackDb/worm/melHap1/trackDb.ra
  • lines changed 70, context: html, text, full: html, text
    wrapping up melHap1 and bruMal1
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Bug #1211 (hg/makefile does not descend into hg/htdocs/): Added htdocsto hg/makefile's BROWSER_BINS, like js, so that all of the targets that use BROWSER_BINS descend into htdocs. Unlike js/makefile, htdocs/makefile does not create the -${USER} directory if it doesn't exist, because Apache config change is required (and permissions for apache/) -- cluster-admin need to handle that. Instead, htdocs' user target checks for the existence of ${DOCUMENTROOT}-${USER} first.
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    Bug #1211 (hg/makefile does not descend into hg/htdocs/): Hiram andBrian pointed out that this is a significant change for mirrors, because our suggested process for static html has been to rsync it from hgdownload, not install from the source tree. Since it is mainly htdocs/style that is tightly bound to the CGIs, I am backing off and changing hg/makefile's BROWSER_BINS to descend only to htdocs/style instead of htdocs.
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    we don't want to be making cgi in encode/encodeValidate any more
• src/hg/ratStuff/mafAddIRows/mafAddIRows.c
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    add a little context to an error message.
• src/hg/utils/refreshNamedSessionCustomTracks/makefile
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    adding -workDir option to be independent of CGI_BIN and update makefile
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    adding -workDir option to be independent of CGI_BIN and update makefile
• src/inc/common.h
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    Added sorting routines for slPairs when the val is a string. Will be used by cv terms whitelist
• src/inc/common.mk
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    add -lpng if libpng.a is not found
• src/lib/common.c
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    Added sorting routines for slPairs when the val is a string. Will be used by cv terms whitelist
• src/lib/net.c
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    putting parentheses around the arguments so printf checking will be happy
• src/lib/osunix.c
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    obscure error messages need to identify themselves
• src/product/README.building.source
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    update with references to other resources
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    add note about libpng difficulties
• src/product/scripts/README
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    update with references to other resources
• src/tracks/makefile
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    Removing hardcoded -lpg from L because it breaks the build on systemsthat don't have libpng. inc/common.mk does some wildcard matching to find the appropriate lib for png if it exists.
• src/utils/qa/weeklybld/buildEnv.csh
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    v243 preview2
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    v243 final build
• src/utils/qa/weeklybld/buildGitReports.csh
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    add preview2 (sometimes called review2, don't ax me why)
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    take out the word Biweekly... is there such a thing as triweekly?
• src/utils/qa/weeklybld/doNewReview2.csh
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    add preview2 (sometimes called review2, don't ax me why)
• src/utils/qa/weeklybld/tagPreview2.csh
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    add preview2 (sometimes called review2, don't ax me why)
• src/weblet/counter/makefile
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    Removing hardcoded -lpg from L because it breaks the build on systemsthat don't have libpng. inc/common.mk does some wildcard matching to find the appropriate lib for png if it exists.

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• files changed: 171