All File Changes

v365_base to v366_preview (2018-05-07 to 2018-05-14) v366

• confs/hgwdev.hg.conf
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    0f00c7bef69169794166a9e4e9a1036df08b7daa Sun May 13 01:11:34 2018 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTrackUi/hgTrackUi.c
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    d20789efcf6e484753b9c8a21b1dd8db40961215 Wed May 9 12:45:38 2018 -0700
    Initial commit of gnomAD track on hg19, refs #18951
• src/hg/hgc/vcfClick.c
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    d20789efcf6e484753b9c8a21b1dd8db40961215 Wed May 9 12:45:38 2018 -0700
    Initial commit of gnomAD track on hg19, refs #18951
• src/hg/htdocs/goldenPath/help/bigChain.html
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    9af92eb4c52f0d76a211deb01d8e54a7e8b13326 Thu May 10 11:00:06 2018 -0700
    Adding missing linebreak between commands.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    a82342b989a97f4e66d80acad265c766e7b01ba0 Mon May 7 11:19:02 2018 -0700
    Making external links open in new windows, also fixing link to Figshare, no ticket
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
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    016aab4539ff047714d8df153b40263790d99d77 Thu May 10 15:30:06 2018 -0700
    Adding notes about magnitude and similarity using descriptions from Braney and input from Kate, no RM
• src/hg/htdocs/staff.html
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    2669e2fa074ab0583c6ef8bf4fc1bafcc67174c5 Mon May 7 11:50:25 2018 -0700
    changing Chris Lee's title
• src/hg/lib/web.c
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    f8ac1b1c8043509e4c4a3bdce70fbaa441ae24ac Wed May 9 13:26:58 2018 -0700
    webTimeStampedLinkToResource: add '../' to link not only when wrapInHtml is true, but also when returning just the link. refs #21403
• src/hg/makeDb/doc/ce4.txt
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    f89810179d12363399f9be991d04fcc7b2216614 Wed May 9 14:35:07 2018 -0700
    add cytoBand track refs #21427
• src/hg/makeDb/doc/hg19.txt
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    d20789efcf6e484753b9c8a21b1dd8db40961215 Wed May 9 12:45:38 2018 -0700
    Initial commit of gnomAD track on hg19, refs #18951
• src/hg/makeDb/doc/hg38/hg38.txt
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    8a67fda1d2857f9737b557353ca40c16665e2652 Wed May 9 15:49:00 2018 -0700
    Finished rmskJoined update, refs #18273
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    5a952022a8a6f8ed82907e16d01144fceb228c5c Wed May 9 16:35:33 2018 -0700
    Add new rmskJoinedCurrent to composite, refs #18273
• src/hg/makeDb/doc/makeEnsembl.txt
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    035d2a8e4dbf82606638fe608a694ab2604fcc59 Wed May 9 13:22:38 2018 -0700
    ensGene v92 update refs #21421
• src/hg/makeDb/doc/xenTro1.txt
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    792c8f921fa75f71bb7708997e2214740ded3d80 Wed May 9 14:42:03 2018 -0700
    adding cytoBandIdeo table refs #21427
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
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    9dabef2bcd6f1de9e01e9f0e9526df10b0287668 Tue May 8 15:10:10 2018 -0700
    ccds changing things again
• src/hg/makeDb/genbank/src/ccds/createTables.sql
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    9dabef2bcd6f1de9e01e9f0e9526df10b0287668 Tue May 8 15:10:10 2018 -0700
    ccds changing things again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
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    9dabef2bcd6f1de9e01e9f0e9526df10b0287668 Tue May 8 15:10:10 2018 -0700
    ccds changing things again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
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    9dabef2bcd6f1de9e01e9f0e9526df10b0287668 Tue May 8 15:10:10 2018 -0700
    ccds changing things again
• src/hg/makeDb/schema/all.joiner
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    ee6c06ddf9029aa92ce4fd45d820b63a7112f090 Wed May 9 13:27:13 2018 -0700
    Adding gnomadVariants to tablesIgnored for hg19, refs #18951
• src/hg/makeDb/trackDb/drosophila/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    39c87731dbe697a5fa7161b2c8bf185fafd5a828 Tue May 8 08:54:34 2018 -0700
    Updating redirected links for droAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    767abc3a7cea38b2fee764e008e3f6157b8b587c Thu May 10 09:05:15 2018 -0700
    Updating the pennantIcon to be more specific about which tracks were released, no Redmine.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 135, context: html, text, full: html, text
    d20789efcf6e484753b9c8a21b1dd8db40961215 Wed May 9 12:45:38 2018 -0700
    Initial commit of gnomAD track on hg19, refs #18951
  • lines changed 1, context: html, text, full: html, text
    5b957979ca089d5ec2b868adfbee673ff8084733 Thu May 10 10:34:10 2018 -0700
    Nearly forgot release tags for gnomAD, refs #18951
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV28lift37.ra
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    2c8dd5b76c5676cb76cc91a78471b62071bac446 Tue May 8 10:15:42 2018 -0700
    Updating the pennantIcon to specify which GENCODE tracks were updated, no Redmine.
  • lines changed 1, context: html, text, full: html, text
    767abc3a7cea38b2fee764e008e3f6157b8b587c Thu May 10 09:05:15 2018 -0700
    Updating the pennantIcon to be more specific about which tracks were released, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/description.html
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    c20c3fd337fc91238582296a9f5231af8a00d278 Tue May 8 15:56:34 2018 -0700
    correcting labels per Kim Pruitt request refs #17313
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    767abc3a7cea38b2fee764e008e3f6157b8b587c Thu May 10 09:05:15 2018 -0700
    Updating the pennantIcon to be more specific about which tracks were released, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV28.ra
  • lines changed 1, context: html, text, full: html, text
    2c8dd5b76c5676cb76cc91a78471b62071bac446 Tue May 8 10:15:42 2018 -0700
    Updating the pennantIcon to specify which GENCODE tracks were updated, no Redmine.
  • lines changed 1, context: html, text, full: html, text
    767abc3a7cea38b2fee764e008e3f6157b8b587c Thu May 10 09:05:15 2018 -0700
    Updating the pennantIcon to be more specific about which tracks were released, no Redmine.
• src/hg/makeDb/trackDb/joinedRmskComposite.ra
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    5a952022a8a6f8ed82907e16d01144fceb228c5c Wed May 9 16:35:33 2018 -0700
    Add new rmskJoinedCurrent to composite, refs #18273
• src/hg/makeDb/trackDb/spMut.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/tetraodon/gaze.html
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    ff5472a08001e4a48efb1a2a58fa9f08f3e1e91c Mon May 14 09:50:49 2018 -0700
    Updating redirected links found by the uiLinks cronjob for tetNig2, no Redmine.
• src/hg/makeDb/trackDb/tetraodon/tetNig2/gold.html
  • lines changed 1, context: html, text, full: html, text
    ff5472a08001e4a48efb1a2a58fa9f08f3e1e91c Mon May 14 09:50:49 2018 -0700
    Updating redirected links found by the uiLinks cronjob for tetNig2, no Redmine.
• src/hg/makeDb/trackDb/tetraodon/xenoMrna.html
  • lines changed 2, context: html, text, full: html, text
    ff5472a08001e4a48efb1a2a58fa9f08f3e1e91c Mon May 14 09:50:49 2018 -0700
    Updating redirected links found by the uiLinks cronjob for tetNig2, no Redmine.
• src/hg/makeDb/trackDb/uniprot.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce10/gap.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce10/gold.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce4/trackDb.5way.ra
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    07184c7bf381e5720db1e3767620f16586f59823 Wed May 9 14:36:09 2018 -0700
    reset name for Summary table refs #21427
• src/hg/makeDb/trackDb/worm/refGene.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/rmsk.html
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    660c4cff7e59477ec172b4d8083157276c88b337 Thu May 10 09:37:57 2018 -0700
    Updating redirected links for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.5way.ra
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    2b6de6ea7a4d646dbca0ed53f0d7825cdd36cc2a Wed May 9 14:37:24 2018 -0700
    there is no table for multiz5waySummary refs #21427
• src/hg/makefile
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    af0e5f0ffb684b1ff714f2131501e5ac06326ba0 Fri May 11 09:29:20 2018 -0700
    Adding Galt's agpMergeChromScaf to top-level build.
• src/hg/phyloPng/phyloPng.c
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    6992d44bfe238ffb2c2d559b23cf739bee503fda Fri May 11 15:27:50 2018 -0700
    Adding a clear button to phyloPng and changing the default tree, refs #17322
• src/hg/utils/automation/EnsGeneAutomate.pm
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    fb8e3d22bcb753fa83d44194c81fa4169c8ce65b Tue May 8 11:59:07 2018 -0700
    adding v92 definitions refs #21421
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    f6c2631c4c4e45fbef055b1e1f5717d7e09c9923 Tue May 8 15:09:26 2018 -0700
    fixing v92 definitions refs #21421
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    7777e0f44fdd1a2715f6d452de0ee866d71ec83d Tue May 8 15:14:44 2018 -0700
    fixing v92 definitions refs #21421
• src/hg/utils/automation/ensGene/anoGam3.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/aotNan1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/cavApe1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/cavPor3.ensGene.ra
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    5b89e8dcb565567840d82f90a2bebb5768ea1d3a Wed May 9 12:16:29 2018 -0700
    updates to new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/cebCap1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/cerAty1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/chiLan1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/colAng1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/criGriChoV1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/criGriChoV2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/danRer11.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/dipOrd2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/dm6.ensGene.ra
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    5b89e8dcb565567840d82f90a2bebb5768ea1d3a Wed May 9 12:16:29 2018 -0700
    updates to new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/felCat8.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/ficAlb1.ensGene.ra
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    5b89e8dcb565567840d82f90a2bebb5768ea1d3a Wed May 9 12:16:29 2018 -0700
    updates to new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/fukDam1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/gorGor4.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/hetGla1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/hetGla2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/jacJac1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/macFas5.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/macNem1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/manLeu1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/mesAur1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/micMur3.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/micOch1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/nanGal1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/nomLeu3.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/octDeg1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/ornAna2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/panPan2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/panTro5.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/papAnu3.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/papAnu4.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/perManBai1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/proCoq1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/rhiBie1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/rhiRox1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/saiBol1.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/speTri2.ensGene.ra
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    5b89e8dcb565567840d82f90a2bebb5768ea1d3a Wed May 9 12:16:29 2018 -0700
    updates to new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/susScr11.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/hg/utils/automation/ensGene/tarSyr2.ensGene.ra
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    e1b5d7fa6fbca8193f7fae37198ff3fd86692541 Wed May 9 12:19:01 2018 -0700
    new definitions for Ensembl genes refs #21421
• src/inc/cheapcgi.h
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    6992d44bfe238ffb2c2d559b23cf739bee503fda Fri May 11 15:27:50 2018 -0700
    Adding a clear button to phyloPng and changing the default tree, refs #17322
• src/inc/common.mk
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    bfe0a60efa02b404843bb9465cea04d6c056ceb6 Tue May 8 09:15:10 2018 -0700
    honor CC if set and watch out for SSL_DIR existing from user suggestion no redmine
• src/lib/cheapcgi.c
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    6992d44bfe238ffb2c2d559b23cf739bee503fda Fri May 11 15:27:50 2018 -0700
    Adding a clear button to phyloPng and changing the default tree, refs #17322
• src/lib/phyloTree.c
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    6992d44bfe238ffb2c2d559b23cf739bee503fda Fri May 11 15:27:50 2018 -0700
    Adding a clear button to phyloPng and changing the default tree, refs #17322
• src/parasol/makefile
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    fef8ba0be8818869f8db954c0e59d7ba63f3dd6e Mon May 7 11:05:27 2018 -0700
    better rsync command to avoid warning message about the /cluster/bin/x86_64 directory not changing with requested refs #21332
• src/utils/qa/weeklybld/buildEnv.csh
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    ff455d3a562f793e221ae8fcabddd71830490118 Mon May 14 10:04:13 2018 -0700
    v366 preview1 refs #21332
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    ac44b3995a05d341c86b2dcf8ff2e792acd30d1c Mon May 7 11:19:55 2018 -0700
    archive the contents of hgcentral refs #21332
• src/utils/qa/weeklybld/buildUtils.csh
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    ee42d7f6eee7ca59b3869975c6a555434263244e Mon May 7 11:11:15 2018 -0700
    fixup parasol make since it was added to userApps refs #21332

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