All File Changes

v238_preview to v238_base (2010-08-10 to 2010-08-17) v238

• src/cdnaAli/g2cCheck/makefile
  • lines changed 7, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/blastToPsl/makefile
  • lines changed 2, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 1, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
  • lines changed 8, context: html, text, full: html, text
    properly compile target for test target and cleanup after
• src/hg/blastToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    properly compile target for test target and cleanup after
• src/hg/cartDump/cartDump.c
  • lines changed 4, context: html, text, full: html, text
    Now that CART_VAR_EMPTY exists, cartDump should accept it just like it accepts 'n/a'
• src/hg/embossToPsl/makefile
  • lines changed 4, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 6, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 11, context: html, text, full: html, text
    add solexa pair fastq views
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Updated Treatment Androgen and Estrogen with appropriate description. Changed display matrix labels of treatments for tracks.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 21, context: html, text, full: html, text
    back out my changes from yesterday
  • lines changed 22, context: html, text, full: html, text
    remove arguments to pass in organism since these are specified in the cv.ra
• src/hg/encode/makefile
  • lines changed 2, context: html, text, full: html, text
    added paraMd5sum to the makefile
• src/hg/encode/paraMd5sum/makefile
  • lines changed 23, context: html, text, full: html, text
    parasolized version of md5sum
• src/hg/encode/paraMd5sum/md5sumWrapper
  • lines changed 3, context: html, text, full: html, text
    parasolized version of md5sum
• src/hg/encode/paraMd5sum/paraMd5sum
  • lines changed 92, context: html, text, full: html, text
    parasolized version of md5sum
• src/hg/estOrient/makefile
  • lines changed 13, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/fishClones/makefile
  • lines changed 11, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/genePredHisto/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 13, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/genePredHisto/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    properly use ../testBinary in test makefiles
• src/hg/genePredSingleCover/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 11, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/genePredSingleCover/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    properly use ../testBinary in test makefiles
• src/hg/genePredToMafFrames/makefile
  • lines changed 1, context: html, text, full: html, text
    properly clean everything during clean target
  • lines changed 11, context: html, text, full: html, text
    fixup test target to use compile and to clean up after test
• src/hg/hgChroms/makefile
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • lines changed 2, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • lines changed 2, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated otherOrgs.ra for hg19, mm9, rn4, ce6, dm3, and sacCer2 to bring them to the latest state to match the xxBlastTab tables rebuilt for those 6 genomes.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Adding trackHash parameter to some new code.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixed missing ENCODE Gencode bug by using trackHash instead of tdbExtras
  • lines changed 65, context: html, text, full: html, text
    Removed unneeded links from blubar for PDF/PS page and left justified the links
  • lines changed 12, context: html, text, full: html, text
    Added Bluebar of links to top of PS/PDF page and 'Return to Browser' button. This is because returning from ps/pdf page to image using back button erases dragReorder changes.
  • lines changed 3, context: html, text, full: html, text
    Changed tooltip for sideButton to make sure shortLabel is seen first, as per QA request
  • lines changed 41, context: html, text, full: html, text
    move trackDbJson code into imageV2.c and print it out from w/n imageBoxDraw to fix problems with subtracks
  • lines changed 22, context: html, text, full: html, text
    Extended limitedVisFromComposite() because findTracks calls it when composite itself is hidden
  • lines changed 42, context: html, text, full: html, text
    Fixed bug when SUBTRACKS_HAVE_VIS was on and wigMafs triggered infinite loop
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    move trackDbJson code into imageV2.c and print it out from w/n imageBoxDraw to fix problems with subtracks
• src/hg/hgTracks/imageV2.c
  • lines changed 31, context: html, text, full: html, text
    If dragReordered, successive newly visible tracks should appear below others
  • lines changed 21, context: html, text, full: html, text
    Changed tooltip for sideButton to make sure shortLabel is seen first, as per QA request
  • lines changed 36, context: html, text, full: html, text
    move trackDbJson code into imageV2.c and print it out from w/n imageBoxDraw to fix problems with subtracks
  • lines changed 13, context: html, text, full: html, text
    Moved some style settings to cheapcgi.c
• src/hg/hgTracks/imageV2.h
  • lines changed 10, context: html, text, full: html, text
    Fixed bug when SUBTRACKS_HAVE_VIS was on and wigMafs triggered infinite loop
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    add some items to excludeVars
• src/hg/hgTracks/searchTracks.c
  • lines changed 2, context: html, text, full: html, text
    Hidden vs. seen controls, id should not equal name
  • lines changed 41, context: html, text, full: html, text
    Needed to change 'sel' and 'vis' logic extensively to make findTracks play nice with composites and non-subtracks
  • lines changed 87, context: html, text, full: html, text
    Removed the CB_SELECTION ifndefs
  • lines changed 6, context: html, text, full: html, text
    clicks in menu bar now work
  • lines changed 45, context: html, text, full: html, text
    implement -/+ buttons
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Fixing off-by-one bug in snp's UCSC predicted function (when - strand last base of codon is on a different exon) reported by user Ivan Adzhubey [Mail Lists - ML - MLQ #650].
• src/hg/htdocs/ENCODE/antibodies.html
  • lines changed 1, context: html, text, full: html, text
    changed Top link double arrow to single arrow to match Tim's composite navigation links
• src/hg/htdocs/ENCODE/cellTypes.html
  • lines changed 1, context: html, text, full: html, text
    changed Top link double arrow to single arrow to match Tim's composite navigation links
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 1, context: html, text, full: html, text
    changed Top link double arrow to single arrow to match Tim's composite navigation links
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 55, context: html, text, full: html, text
    fixed the ordering of regulation track downloads to be in alphabetical order
  • lines changed 27, context: html, text, full: html, text
    added new section for the regulation super-track hg18 release
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 15, context: html, text, full: html, text
    changed Top link double arrow to single arrow to match Tim's composite navigation links
  • lines changed 29, context: html, text, full: html, text
    Updated the registered variables page to include seqPlatform.
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/indexNews.html
  • lines changed 99, context: html, text, full: html, text
    removed older items
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    trying it without -q so people are aware of the updates happening
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 2, context: html, text, full: html, text
    Further tweaks in the mysterious black arts of css
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    Keeping track of vars chasnged by cgi requires the concept of CART_VAR_EMPTY
  • lines changed 16, context: html, text, full: html, text
    Added cartTdbTreeCleanupOverrides to cleanup subtrack settings when composite/view settings change
• src/hg/inc/hui.h
  • lines changed 12, context: html, text, full: html, text
    Needed to make subtrack four state CB logic available to hgTracks
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    "New version number v238"
• src/hg/js/hgTracks.js
  • lines changed 15, context: html, text, full: html, text
    Hidden vs. seen controls, id should not equal name
  • lines changed 32, context: html, text, full: html, text
    changes to make changing visibility work for subtracks
  • lines changed 88, context: html, text, full: html, text
    Needed to change 'sel' and 'vis' logic extensively to make findTracks play nice with composites and non-subtracks
  • lines changed 1, context: html, text, full: html, text
    Tabs were shown as divs before being set up. Now they are hidden until set up
  • lines changed 2, context: html, text, full: html, text
    disable postToSaveSettings in search form page (fixes problem where top menu bar didn't work
  • lines changed 14, context: html, text, full: html, text
    add delSearchSelect and addSearchSelect
• src/hg/js/hui.js
  • lines changed 4, context: html, text, full: html, text
    Made subtrack DnD a little more consistent with imageV2 DnD
• src/hg/js/jquery.tablednd.js
  • lines changed 1, context: html, text, full: html, text
    Fixed bug affecting subtrack list DnD but not trackImage DnD
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    trying it without -q so people are aware of the updates happening
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    Fixed a few comments
• src/hg/lib/cart.c
  • lines changed 72, context: html, text, full: html, text
    Keeping track of vars chasnged by cgi requires the concept of CART_VAR_EMPTY
  • lines changed 157, context: html, text, full: html, text
    Added cartTdbTreeCleanupOverrides to cleanup subtrack settings when composite/view settings change
• src/hg/lib/ensGtp.sql
  • lines changed 2, context: html, text, full: html, text
    need 24 characters not just 23 for other name
  • lines changed 3, context: html, text, full: html, text
    longer names for ensembl proteins first seen in mm9
• src/hg/lib/hgSeq.c
  • lines changed 1, context: html, text, full: html, text
    prevent opening an sql connection for each sequence retrieved by the table browser
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    change tooltip for file downloads
  • lines changed 17, context: html, text, full: html, text
    Needed to make subtrack four state CB logic available to hgTracks
  • lines changed 19, context: html, text, full: html, text
    make link in ENCODE ... metadata section go straight to the file
• src/hg/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    can remove the loader symlink after the custom track test is done to keep source tree cleaner
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Added cartTdbTreeCleanupOverrides to cleanup subtrack settings when composite/view settings change
• src/hg/lib/wigDataStream.c
  • lines changed 7, context: html, text, full: html, text
    use hAllocConn instead of sqlConnect
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 22, context: html, text, full: html, text
    build some metadata
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAffyLoc.release1.notes
  • lines changed 148, context: html, text, full: html, text
    release notes for wgEncodeAffyRnaLoc
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisDnaPet.release1.notes
  • lines changed 74, context: html, text, full: html, text
    notes for hg19 release1 of Gis DNA=-pet
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 6, context: html, text, full: html, text
    update note about lifting Ensembl EF2 sequence to sacCer2 coordinates
  • lines changed 39, context: html, text, full: html, text
    done with all organisms for v59
  • lines changed 19, context: html, text, full: html, text
    finished the ce9 ensGenes
  • lines changed 269, context: html, text, full: html, text
    finished with the broken bits
  • lines changed 850, context: html, text, full: html, text
    starting ensembl v59 update
• src/hg/makeDb/doc/mm8.txt
  • lines changed 20, context: html, text, full: html, text
    re-running mm8->mm9 liftover with improved process
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    reenable cavPor3 alignments
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    reenable cavPor3
• src/hg/makeDb/hgTomRough/makefile
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    move UwAffyExonArray metadata to metadb from trackDb
  • lines changed 1, context: html, text, full: html, text
    metadata for regulation rainbow clusters
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeReg.ra
  • lines changed 61, context: html, text, full: html, text
    metadata for regulation rainbow clusters
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 1201, context: html, text, full: html, text
    move UwAffyExonArray metadata to metadb from trackDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    adding wgEncodeUwAffyExonArray.ra to make files of beta and public so it will use metaDB
  • lines changed 1, context: html, text, full: html, text
    adding metaDb for ENCODE Regulation Track to beta and public
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeReg.ra
  • lines changed 61, context: html, text, full: html, text
    copying metDb .ra files into beta and public so these tracks will use metaDb on beta and the RR
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 1201, context: html, text, full: html, text
    copying metDb .ra files into beta and public so these tracks will use metaDb on beta and the RR
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    adding wgEncodeUwAffyExonArray.ra to make files of beta and public so it will use metaDB
  • lines changed 1, context: html, text, full: html, text
    adding metaDb for ENCODE Regulation Track to beta and public
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeReg.ra
  • lines changed 61, context: html, text, full: html, text
    copying metDb .ra files into beta and public so these tracks will use metaDb on beta and the RR
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 1201, context: html, text, full: html, text
    copying metDb .ra files into beta and public so these tracks will use metaDb on beta and the RR
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 71, context: html, text, full: html, text
    move UwAffyExonArray metadata to metadb from trackDb
  • lines changed 40, context: html, text, full: html, text
    removed release tags for the release of the regulatory track
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    updated the text so that it had the meaning that Jim wanted
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
  • lines changed 1, context: html, text, full: html, text
    removed extra </p> that was breaking up a paragraph
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 7, context: html, text, full: html, text
    change dataVersion
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Corrected Typo of labExpId as labExpIdn
  • lines changed 4, context: html, text, full: html, text
    Reverted some changes to metaData protocol lines that were put in by accident
  • lines changed 12, context: html, text, full: html, text
    Updated metadata that was incorrect and previously looked over.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 230, context: html, text, full: html, text
    Added additional celltype Melano that was previosuly missing
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 135, context: html, text, full: html, text
    Added subId=2108 for SYDH Histone data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1365, context: html, text, full: html, text
    Cleaned up inputType from metaDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    making felCat3 chain/Nets for hg19 and mm9 have o_db rather than o_organism
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    putting felCat4 chain/net in human placental track as well as making the short label for all chain/nets be 'cat' instead of 'felCat4'
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra
  • lines changed 19, context: html, text, full: html, text
    Added subId=2108 for SYDH Histone data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
  • lines changed 4, context: html, text, full: html, text
    add some release notes declaring that these results were lifted up from hg18
  • lines changed 5, context: html, text, full: html, text
    fixed html missing end tag
  • lines changed 15, context: html, text, full: html, text
    Added verbage to say that we did not lift over the signals
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    added release alpha,beta tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 18, context: html, text, full: html, text
    Updated track description and track names, tried to make sort work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 27, context: html, text, full: html, text
    Updated track description and track names, tried to make sort work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Treatment Androgen and Estrogen with appropriate description. Changed display matrix labels of treatments for tracks.
  • lines changed 30, context: html, text, full: html, text
    Added additional celltype Melano that was previosuly missing
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Treatment Androgen and Estrogen with appropriate description. Changed display matrix labels of treatments for tracks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 81, context: html, text, full: html, text
    revoked submissions 1803, 1798, 1809
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    trying it without -q so people are aware of the updates happening
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 49, context: html, text, full: html, text
    Cleaned up inputType from metaDb for mouse
  • lines changed 1204, context: html, text, full: html, text
    Update Mouse metaData to remove human data cell types
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 296, context: html, text, full: html, text
    Cleaned up inputType from metaDb for mouse
  • lines changed 14982, context: html, text, full: html, text
    Update Mouse metaData to remove human data cell types
  • lines changed 1843, context: html, text, full: html, text
    Updated metaData with missing data
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    making felCat3 chain/Nets for hg19 and mm9 have o_db rather than o_organism
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    putting felCat4 chain/net in human placental track as well as making the short label for all chain/nets be 'cat' instead of 'felCat4'
• src/hg/mouseStuff/simpleChain/makefile
  • lines changed 6, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/nci60/makefile
  • lines changed 3, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/overlapSelect/makefile
  • lines changed 5, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslCDnaFilter/makefile
  • lines changed 5, context: html, text, full: html, text
    fixing test target in fixed makefiles
  • lines changed 8, context: html, text, full: html, text
    fixing makefiles to not leave garbage around
• src/hg/pslDiff/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing test target in fixed makefiles
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• src/hg/pslFilterPrimers/makefile
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• src/hg/pslPairs/makefile
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    fixing makefiles to not leave garbage around
• src/hg/pslPartition/makefile
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    properly clean everything during clean target
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    fixup test target to use compile and to clean up after test
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• src/hg/pslQuickFilter/makefile
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    fixing makefiles to not leave garbage around
• src/hg/pslSwap/makefile
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    fixing test target in fixed makefiles
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• src/hg/sage/makefile
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    fixing makefiles to not leave garbage around
• src/hg/snp/snpValid/makefile
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    fixing makefiles to not leave garbage around
• src/hg/spideyToPsl/makefile
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    fixing test target in fixed makefiles
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• src/hg/uniqSize/makefile
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• src/hg/updateStsInfo/makefile
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• src/hg/utils/automation/ensGeneScaffolds.pl
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    allow scaffold names of ^Scaffold for macEug1
• src/hg/utils/mutationClassifier/mutationClassifier.c
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    support -bindingSites option
• src/inc/cheapcgi.h
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    Extended commonCssStyles and made amenable to printf/hgPrintf
• src/inc/common.mk
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    adding -lcrypto to -lssl
• src/lib/cheapcgi.c
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    Name is now optional on drop down select. This was necessary to make findTracks behave
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    Extended commonCssStyles and made amenable to printf/hgPrintf
• src/lib/errabort.c
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    Missed sheltering the include execinfo.h within BACKTRACE_EXISTS define
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    can remove fetchUrlTest at end of tests and during clean
• src/makefile
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    trying it without -q so people are aware of the updates happening
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    no need to mention a version or date stamp
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    point to updateHtml.sh instead of the rsync to fetch htdocs
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    updated to eliminate references to a CDROM
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    fixup permission grant statements to use FILE properly
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    irrelevant files since changing to git
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    fixup gbdb no longer relevant in 2010
• src/product/makefile
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    remove references to CVS commands
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    no longer required in git world
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    remove references to CVS commands
• src/product/scripts/dbTrashCleaner.sh
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    contents have been subsumed into trashCleaner.csh
• src/product/scripts/kentSrcUpdate.sh
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    update to git commands
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    fixing path to old sandbox that no longer exists
• src/utils/qa/makefile
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    trying it without -q so people are aware of the updates happening
• src/utils/qa/weeklybld/buildEnv.csh
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    v237 final build (for reals this time ;-)
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• src/xenoAli/dynAlign/makefile
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