All File Changes

v284_preview2 to v284_base (2013-05-21 to 2013-05-27) v284

• src/gfClient/makefile
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    fixup makefile to new minimal standard refs #9149
• src/gfServer/makefile
  • lines changed 16, context: html, text, full: html, text
    fixup makefile to new minimal standard refs #9149
• src/hg/geneBounds/makefile
  • lines changed 8, context: html, text, full: html, text
    fixup parallel build rules refs #9104
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    add some blue bars for duplications in HAL snakes
• src/hg/hgTracks/pubsTracks.c
  • lines changed 2, context: html, text, full: html, text
    changes after code review #10861
• src/hg/hgTracks/snakeTrack.c
  • lines changed 42, context: html, text, full: html, text
    add some blue bars for duplications in HAL snakes
• src/hg/hgc/hgc.c
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    removed unneeded cartWebEnd call
• src/hg/hgc/pubs.c
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    changes after code review #10861
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    added comment code review #10861
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 12, context: html, text, full: html, text
    Replace item linking to OpenHelix (now charging) with more generic user info link
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    Adding link to Spark Tool (and removing bullet I mistakenly had around reference) for ENCODE portal May update refs #10760
• src/hg/htdocs/ENCODE/externalTools.html
  • lines changed 389, context: html, text, full: html, text
    Adding new link on softwareTools.html to point to new externalTools page for ENCODE May 2013 update refs #10760
  • lines changed 27, context: html, text, full: html, text
    Small edits to grammar and style for new externalTools.html page for ENCODE May Portal update refs #10760
  • lines changed 3, context: html, text, full: html, text
    Grammar corrrection. refs #10760.
  • lines changed 1, context: html, text, full: html, text
    Minor usage fix. refs #10760
• src/hg/htdocs/ENCODE/index.html
  • lines changed 19, context: html, text, full: html, text
    Adding update to ENCODE/index.html about new publications refs #10760
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 311, context: html, text, full: html, text
    Adding publications for May 2013 ENCODE portal update, refs #10760
  • lines changed 1, context: html, text, full: html, text
    Update date updated. refs #10760
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 741, context: html, text, full: html, text
    Adding publications for May 2013 ENCODE portal update, refs #10760
  • lines changed 1, context: html, text, full: html, text
    Update date updated. refs #10760
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 2, context: html, text, full: html, text
    Fix spelling errs. refs #10760
• src/hg/htdocs/ENCODE/softwareTools.html
  • lines changed 11, context: html, text, full: html, text
    Adding new link on softwareTools.html to point to new externalTools page for ENCODE May 2013 update refs #10760
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 18, context: html, text, full: html, text
    Update Education & Outreaches page to highlight new NHGRI ENCODE tutorials. refs #10760
  • lines changed 13, context: html, text, full: html, text
    1. Highlight quick ref card also. Trim lines to 100 chars. refs #10760
  • lines changed 1, context: html, text, full: html, text
    Add update timestamp. refs #10760
  • lines changed 1, context: html, text, full: html, text
    Add link to new NHGRI tutorials page. refs #10760
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    releasing Gibbon/nomLeu3 browser refs #9812
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    releasing Gibbon/nomLeu3 browser refs #9812
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 134, context: html, text, full: html, text
    Updated the haplotypes help page to reflect recent changes requested by Brooke Pauline and B0b. At this point I am only anticipating one additional update to the 'population score' portion of the document.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    releasing Gibbon/nomLeu3 browser refs #9812
• src/hg/htdocs/indexNews.html
  • lines changed 35, context: html, text, full: html, text
    releasing Gibbon/nomLeu3 browser refs #9812
• src/hg/htdocs/staff.html
  • lines changed 10, context: html, text, full: html, text
    Added self to staff page, moved Cricket to alumni
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v284
• src/hg/lib/haplotypes.c
  • lines changed 16, context: html, text, full: html, text
    Fixed a popScore problem seen on chrY and fixed the sort of population distribution columns.
  • lines changed 93, context: html, text, full: html, text
    Population score should now be set. Using the variance version of fixation index which is proving to identify interesting gene models.
• src/hg/lib/hdb.c
  • lines changed 9, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/hg/lib/hgFind.c
  • lines changed 6, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    HTML formatting correction, fixes extra space before comman in cell type lists, found by Brooke during QA. refs #10097
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    clone a string in response to a code review #1080
  • lines changed 56, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    HTML formatting correction, fixes extra space before comman in cell type lists, found by Brooke during QA. refs #10097
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 26, context: html, text, full: html, text
    Redo clustering with HA-E2F1 merged with E2F1 (re Peggy Farnham). Two antibodies same factor. refs #10097
  • lines changed 5, context: html, text, full: html, text
    Redo clustering with HA-E2F1 merged with E2F1 (as per Peggy Farnham). Stage this version for release (V6 -> V3). Initial work on track description. refs #10097
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 121, context: html, text, full: html, text
    v71 update done refs #10746
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • lines changed 1, context: html, text, full: html, text
    hgdownload-sd will no longer tolerate rsh for connections. Use ssh to rsync downloads.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    turning on genbank updates on the RR for nomLeu3 new release refs #9812
• src/hg/makeDb/makefile
  • lines changed 20, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken link on wgEncodeDNAseSuper.html page, making relative, MLQ refs #10894
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 1, context: html, text, full: html, text
    Fix typo caught by Flo Pauli at HAIB. refs #10447.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 17, context: html, text, full: html, text
    Redo clustering with HA-E2F1 merged with E2F1 (re Peggy Farnham). Two antibodies same factor. refs #10097
  • lines changed 9, context: html, text, full: html, text
    Redo clustering with HA-E2F1 merged with E2F1 (as per Peggy Farnham). Stage this version for release (V6 -> V3). Initial work on track description. refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 67, context: html, text, full: html, text
    Redo clustering with HA-E2F1 merged with E2F1 (as per Peggy Farnham). Stage this version for release (V6 -> V3). Initial work on track description. refs #10097
• src/hg/makefile
  • lines changed 72, context: html, text, full: html, text
    expanding the list of userApps in hg refs #9104
  • lines changed 48, context: html, text, full: html, text
    updating userApps list refs #9149
  • lines changed 1, context: html, text, full: html, text
    updating userApps buildlist refs #9149
  • lines changed 10, context: html, text, full: html, text
    updating userApps buildlist refs #9149
  • lines changed 3, context: html, text, full: html, text
    updating userApps buildlist refs #9149
  • lines changed 6, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/hg/mouseStuff/makefile
  • lines changed 55, context: html, text, full: html, text
    updating userApps buildlist refs #9149
  • lines changed 19, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/hg/ratStuff/makefile
  • lines changed 40, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/hg/sqlEnvTest.sh
  • lines changed 5, context: html, text, full: html, text
    approaching something useful refs #9104
• src/hg/utils/makefile
  • lines changed 46, context: html, text, full: html, text
    updating userApps list refs #9149
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    updating userApps buildlist refs #9149
• src/inc/common.mk
  • lines changed 51, context: html, text, full: html, text
    adding auto detection of mysql lib installs and more userApps source fetch refs #9104
• src/inc/trix.h
  • lines changed 1, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
  • lines changed 1, context: html, text, full: html, text
    oops typo!
• src/inc/udc.h
  • lines changed 3, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/lib/memgfx.c
  • lines changed 9, context: html, text, full: html, text
    fix problem with clipping rectangles reported in refs #10847
• src/lib/trix.c
  • lines changed 50, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/lib/udc.c
  • lines changed 35, context: html, text, full: html, text
    added TRIX search for track hubs. UDC'ified trix library. Refs #10426
• src/makefile
  • lines changed 3, context: html, text, full: html, text
    fixup parallel build rules refs #9104
  • lines changed 8, context: html, text, full: html, text
    approaching something useful refs #9104
  • lines changed 8, context: html, text, full: html, text
    HG_APPLIST has moved to target userApps in hg/makefile refs #9104
  • lines changed 16, context: html, text, full: html, text
    updating userApps buildlist refs #9149
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    updating userApps buildlist refs #9149
• src/parasol/makefile
  • lines changed 22, context: html, text, full: html, text
    parallize the para bin build refs #9104
• src/userApps/GenomeBrowserLicense.pdf
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    begin to construct the Makefile and add the license statements refs #9104
• src/userApps/Makefile
  • lines changed 19, context: html, text, full: html, text
    begin to construct the Makefile and add the license statements refs #9104
  • lines changed 27, context: html, text, full: html, text
    approaching something useful refs #9104
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    adding parasol to the userApps build refs #9104
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    construct the kentUtils.Documentation.txt from the commands usage messages refs #9104
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    OK to ignore errors on make clean due to missing directories refs #9104
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    fixup the Makefile so it will correctly bootstrap itself, and expand the README, refs #9149
• src/userApps/README
  • lines changed 69, context: html, text, full: html, text
    begin structure to fetch and build the user apps at an external location
  • lines changed 3, context: html, text, full: html, text
    adjusting README instructions and expanding the fetch operation refs #9104
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    updating list of userApps in src/utils refs #9104
  • lines changed 16, context: html, text, full: html, text
    adding parasol to the userApps build refs #9104
  • lines changed 4, context: html, text, full: html, text
    construct the kentUtils.Documentation.txt from the commands usage messages refs #9104
  • lines changed 1, context: html, text, full: html, text
    update comment about resulting size of binaries refs #9104
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    fixup the Makefile so it will correctly bootstrap itself, and expand the README, refs #9149
  • lines changed 4, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/userApps/fetchKentSource.sh
  • lines changed 48, context: html, text, full: html, text
    begin structure to fetch and build the user apps at an external location
  • lines changed 121, context: html, text, full: html, text
    adjusting README instructions and expanding the fetch operation refs #9104
  • lines changed 142, context: html, text, full: html, text
    adding auto detection of mysql lib installs and more userApps source fetch refs #9104
  • lines changed 4, context: html, text, full: html, text
    approaching something useful refs #9104
  • lines changed 1, context: html, text, full: html, text
    adding parasol to the userApps build refs #9104
  • lines changed 3, context: html, text, full: html, text
    updating userApps buildlist refs #9149
• src/userApps/licenseBlat.txt
  • lines changed 12, context: html, text, full: html, text
    begin to construct the Makefile and add the license statements refs #9104
• src/userApps/licenseUcscGenomeBrowser.txt
  • lines changed 26, context: html, text, full: html, text
    begin to construct the Makefile and add the license statements refs #9104
• src/utils/makefile
  • lines changed 123, context: html, text, full: html, text
    fixup parallel build rules refs #9104
  • lines changed 88, context: html, text, full: html, text
    updating list of userApps in src/utils refs #9104
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v284 final build
• src/utils/twoBitDup/makefile
  • lines changed 17, context: html, text, full: html, text
    fixup parallel build rules refs #9104
• src/utils/userApps/mkREADME.sh
  • lines changed 1, context: html, text, full: html, text
    protect this procedure from the hgsql command refs #9104

• lines changed: 3646
• files changed: 105