All File Changes

v355_preview2 to v355_base (2017-09-11 to 2017-09-18) v355

• src/browserbox/root/updateBrowser.sh
  • lines changed 15, context: html, text, full: html, text
    52f0879948e0ddbc84d9cee4952630ebca724f1f Mon Sep 11 14:32:41 2017 -0700
    Adding check for genome-euro proximity to gbib to let them use new genome-euro mysql server, refs #19276
  • lines changed 1, context: html, text, full: html, text
    26cabd382847203149cc8be017ae1dcd5c156a09 Tue Sep 12 09:29:49 2017 -0700
    Fixing genome-euro mysql name, refs #19276
• src/hg/hgCollection/hgCollection.c
  • lines changed 54, context: html, text, full: html, text
    8a6bf192d6c474938510f746fb924393ce236295 Wed Sep 13 17:58:23 2017 -0700
    make visible tracks in hgCollection follow imgOrd in cart. Put collections information in AJAX
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 5, context: html, text, full: html, text
    7b7d273fd3aeee222d5ee8540298ac6dee662605 Wed Sep 13 11:45:23 2017 -0700
    Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's. It can be distracting in large regions. refs #15646
• src/hg/hgTracks/gtexEqtlClusterTrack.c
  • lines changed 17, context: html, text, full: html, text
    948ce415a6e8b218d601cc2034d7ba1b0c56e468 Wed Sep 13 10:39:29 2017 -0700
    Replace colored asterisk with color patch to indicate tissue color. Input from Casey Brown, U Penn. refs #15646
  • lines changed 16, context: html, text, full: html, text
    7b7d273fd3aeee222d5ee8540298ac6dee662605 Wed Sep 13 11:45:23 2017 -0700
    Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's. It can be distracting in large regions. refs #15646
  • lines changed 17, context: html, text, full: html, text
    155896fe22edfc94d4171b7f3f42f4135d2f50a8 Wed Sep 13 13:23:38 2017 -0700
    Add (filter activated) to track label if any track filter is on. refs #15646
  • lines changed 1, context: html, text, full: html, text
    3e8b799ea362787783b55ce6a82623fb3d958ab4 Thu Sep 14 08:44:51 2017 -0700
    Remove partially removed debug statement.
  • lines changed 1, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/hgTracks/hgTracks.c
  • lines changed 47, context: html, text, full: html, text
    8a6bf192d6c474938510f746fb924393ce236295 Wed Sep 13 17:58:23 2017 -0700
    make visible tracks in hgCollection follow imgOrd in cart. Put collections information in AJAX
  • lines changed 1, context: html, text, full: html, text
    dbedb044e0046ef138a753ce84850b69f13c75a1 Thu Sep 14 08:14:24 2017 -0700
    quick fix to crashing bug
• src/hg/hgc/gencodeClick.c
  • lines changed 8, context: html, text, full: html, text
    e60c92aa698eb013b9a226d2d99e3aa719d91928 Wed Sep 13 17:56:43 2017 -0700
    fixed link to Ensembl web site for GENCODE lift37 release
• src/hg/hgc/gtexEqtlClusterClick.c
  • lines changed 5, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
• src/hg/hgc/peakClusters.c
  • lines changed 4, context: html, text, full: html, text
    2c4c9d5fee670cac2d67fd57cac606c4d619a1e6 Thu Sep 14 11:00:37 2017 -0700
    rework code to eliminate complicated double nested div elements refs #20094
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 84, context: html, text, full: html, text
    8f01e5e7b822f27019bc4184f2622f963608158a Wed Sep 13 12:13:28 2017 -0700
    Adding back versions of gbdDescriptions.html and gbdDescriptionsOld.html to support links that point to those locations. refs #20129
• src/hg/htdocs/goldenPath/gbdDescriptionsOld.html
  • lines changed 5866, context: html, text, full: html, text
    8f01e5e7b822f27019bc4184f2622f963608158a Wed Sep 13 12:13:28 2017 -0700
    Adding back versions of gbdDescriptions.html and gbdDescriptionsOld.html to support links that point to those locations. refs #20129
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 17, context: html, text, full: html, text
    ad307ba1358ef62009678deaff677b2d502d6e3d Mon Sep 11 10:32:36 2017 -0700
    Adding info to gbib html help page about updated gbibAddTools command, refs #19276
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 92, context: html, text, full: html, text
    e2516accb4af76f6e0e806a164f43c3d8a1b17a7 Fri Sep 15 15:09:24 2017 -0700
    First pass of adding hosting providers section to track hub help page. Will need to add a similar section to the custom tracks page, as well as links to this section from other help pages, refs #12822
  • lines changed 33, context: html, text, full: html, text
    f644fdab0e1c0efb8d2215242a90cba81ebf0778 Mon Sep 18 10:20:21 2017 -0700
    Fixing some typos, including some pictures of Github, and expanding of advantages and disadvantages of different hosting providers, refs #12822
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    26b91fc1b20aceba42aad6f3df61d437cb974615 Tue Sep 12 14:52:52 2017 -0700
    Announcing the release of the GTEx Transcript Expression tracks for hg19 and hg38. Also adding the date to the Ensembl update announcement. refs #19350
  • lines changed 3, context: html, text, full: html, text
    a655c39e0d3d991d803a1e5db724dce04170e117 Tue Sep 12 15:35:33 2017 -0700
    Adding Kate's suggestions to the announcement, refs #19350
  • lines changed 17, context: html, text, full: html, text
    61709c9195512b99704e25acbb0cc89f272f3e17 Fri Sep 15 14:30:15 2017 -0700
    Staging commented-out snpedia announcements, refs #19811
• src/hg/htdocs/images/githubRawLink.png
  • lines changed 0, context: html, text, full: html, text
    f644fdab0e1c0efb8d2215242a90cba81ebf0778 Mon Sep 18 10:20:21 2017 -0700
    Fixing some typos, including some pictures of Github, and expanding of advantages and disadvantages of different hosting providers, refs #12822
• src/hg/htdocs/images/githubRawUrl.png
  • lines changed 0, context: html, text, full: html, text
    f644fdab0e1c0efb8d2215242a90cba81ebf0778 Mon Sep 18 10:20:21 2017 -0700
    Fixing some typos, including some pictures of Github, and expanding of advantages and disadvantages of different hosting providers, refs #12822
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    26b91fc1b20aceba42aad6f3df61d437cb974615 Tue Sep 12 14:52:52 2017 -0700
    Announcing the release of the GTEx Transcript Expression tracks for hg19 and hg38. Also adding the date to the Ensembl update announcement. refs #19350
  • lines changed 10, context: html, text, full: html, text
    61709c9195512b99704e25acbb0cc89f272f3e17 Fri Sep 15 14:30:15 2017 -0700
    Staging commented-out snpedia announcements, refs #19811
• src/hg/inc/gtexEqtlCluster.h
  • lines changed 5, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/inc/gtexUi.h
  • lines changed 1, context: html, text, full: html, text
    5e3ebd3cd9d33f04a7f04eac381acf6492696549 Wed Sep 13 10:35:16 2017 -0700
    Lower default probability to include all CAVIAR 95% eQtls. Feedback from Casey Brown, U Penn. refs #15646
  • lines changed 8, context: html, text, full: html, text
    7b7d273fd3aeee222d5ee8540298ac6dee662605 Wed Sep 13 11:45:23 2017 -0700
    Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's. It can be distracting in large regions. refs #15646
  • lines changed 1, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    d1c3664c53b17dd2a8394bbed9b13f69df7c43c5 Mon Sep 18 10:49:51 2017 -0700
    New version number v355
• src/hg/inc/web.h
  • lines changed 2, context: html, text, full: html, text
    2c4c9d5fee670cac2d67fd57cac606c4d619a1e6 Thu Sep 14 11:00:37 2017 -0700
    rework code to eliminate complicated double nested div elements refs #20094
• src/hg/lib/cart.c
  • lines changed 9, context: html, text, full: html, text
    acdd3b5efa8944ca173016b6b0ce8170197c80f7 Tue Sep 12 12:48:48 2017 -0700
    check for a disappearing custom hub
• src/hg/lib/gtexEqtlCluster.as
  • lines changed 3, context: html, text, full: html, text
    b704f6ea6af03bdf07246fc691b5c16477b0786b Thu Sep 14 13:28:37 2017 -0700
    Clarify schema description. refs #15646
• src/hg/lib/gtexEqtlCluster.c
  • lines changed 44, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/lib/gtexEqtlCluster.sql
  • lines changed 2, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/lib/gtexUi.c
  • lines changed 23, context: html, text, full: html, text
    7b7d273fd3aeee222d5ee8540298ac6dee662605 Wed Sep 13 11:45:23 2017 -0700
    Add UI setting to toggle display of tissue color patches (for single-tissue eQTL's. It can be distracting in large regions. refs #15646
  • lines changed 1, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/lib/web.c
  • lines changed 15, context: html, text, full: html, text
    2c4c9d5fee670cac2d67fd57cac606c4d619a1e6 Thu Sep 14 11:00:37 2017 -0700
    rework code to eliminate complicated double nested div elements refs #20094
  • lines changed 1, context: html, text, full: html, text
    e0323ab9105d1ab46644efbb1e15cd92c6d8c043 Thu Sep 14 11:03:21 2017 -0700
    use both classes in the open div refs #20094
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 28, context: html, text, full: html, text
    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
  • lines changed 14, context: html, text, full: html, text
    a4282883a88241a9db9fa858cc6e6efa875be553 Fri Sep 15 11:37:31 2017 -0700
    correctly fetch the Hoffman mappability big files refs #19154
• src/hg/makeDb/doc/hg38/snpedia.txt
  • lines changed 13, context: html, text, full: html, text
    8a9f85529515309e935064aa2d53421978687dd7 Fri Sep 15 23:29:29 2017 -0700
    making snpedia a composite with two subtracks, refs #19811
• src/hg/makeDb/doc/mm10.txt
  • lines changed 28, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
  • lines changed 9, context: html, text, full: html, text
    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
  • lines changed 17, context: html, text, full: html, text
    4b0dfefa6446d914c0920d677336d1f5de20e2ea Fri Sep 15 16:12:42 2017 -0700
    Ran updated ncbiRefSeq pipeline on mm10. refs #18997
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.bigMaf.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    640d8d9a8069fc0e500d19239da13bb14f6c61b7 Fri Sep 15 11:09:47 2017 -0700
    Fixing the compGeno group in the mouseStrain hub, no Redmine
• src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs
  • lines changed 37, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 6, context: html, text, full: html, text
    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
  • lines changed 4, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
  • lines changed 5, context: html, text, full: html, text
    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
• src/hg/makeDb/schema/all.joiner
  • lines changed 91, context: html, text, full: html, text
    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
  • lines changed 92, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/scripts/snpedia/bed4Note.as
  • lines changed 10, context: html, text, full: html, text
    8a9f85529515309e935064aa2d53421978687dd7 Fri Sep 15 23:29:29 2017 -0700
    making snpedia a composite with two subtracks, refs #19811
• src/hg/makeDb/scripts/snpedia/makeAll.py
  • lines changed 72, context: html, text, full: html, text
    8a9f85529515309e935064aa2d53421978687dd7 Fri Sep 15 23:29:29 2017 -0700
    making snpedia a composite with two subtracks, refs #19811
• src/hg/makeDb/trackDb/alpaca/vicPac2/gap.html
  • lines changed 1, context: html, text, full: html, text
    5e378834990b6ea15ad5bf4720a2d94d49065adf Thu Sep 14 07:41:12 2017 -0700
    Fixing broken links found by the broken link report for vicPac2, no Redmine
• src/hg/makeDb/trackDb/alpaca/vicPac2/gold.html
  • lines changed 1, context: html, text, full: html, text
    5e378834990b6ea15ad5bf4720a2d94d49065adf Thu Sep 14 07:41:12 2017 -0700
    Fixing broken links found by the broken link report for vicPac2, no Redmine
• src/hg/makeDb/trackDb/blastDm2FB.html
  • lines changed 1, context: html, text, full: html, text
    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/chainCi2.html
  • lines changed 5, context: html, text, full: html, text
    767c3c3a6f1399d8ccf3d339d37597df04cbfe81 Tue Sep 12 08:55:08 2017 -0700
    Fixing broken links found by the broken link report for strPur2, no Redmine
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
  • lines changed 5, context: html, text, full: html, text
    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/drosophila/mrna.html
  • lines changed 6, context: html, text, full: html, text
    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/drosophila/rmsk.html
  • lines changed 1, context: html, text, full: html, text
    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/drosophila/xenoRefGene.html
  • lines changed 3, context: html, text, full: html, text
    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/horse/equCab2/ctgPos2.html
  • lines changed 3, context: html, text, full: html, text
    fbb45914bb205a7af64d5880e2f438adfbd10cd2 Wed Sep 13 08:30:52 2017 -0700
    Fixing broken links found by the broken link report for equCab2, no Redmine.
• src/hg/makeDb/trackDb/horse/equCab2/nscanGene.html
  • lines changed 11, context: html, text, full: html, text
    fbb45914bb205a7af64d5880e2f438adfbd10cd2 Wed Sep 13 08:30:52 2017 -0700
    Fixing broken links found by the broken link report for equCab2, no Redmine.
• src/hg/makeDb/trackDb/human/gtexTranscExpr.html
  • lines changed 1, context: html, text, full: html, text
    6e283588d98137988cf7c2e1e7be17b7e1c81357 Mon Sep 11 12:01:31 2017 -0700
    Removing   to left-justify the barchart image, refs #19350
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 2, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 28, context: html, text, full: html, text
    6f4f71f60e9628b1e5887b5ed6099746292a142c Fri Sep 15 10:02:10 2017 -0700
    consistently used trackDb.gencode.ra for gencode track ra includes. This will lead to more automation
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    54865dd4a5a0e78adc818a6f8c19c02cc21bc581 Mon Sep 11 15:48:10 2017 -0700
    Removing score filter for cosmic v82 tracks, all items have a score of 0. refs #19932
  • lines changed 15, context: html, text, full: html, text
    40a34c50eafab3d08708d91c765900d7231eeba2 Tue Sep 12 14:13:36 2017 -0700
    Making cosmic v82 track public, removing old v81 track, refs #19932
  • lines changed 3, context: html, text, full: html, text
    d09b392333a2f5d2f943f2f36dad4be0a477381e Thu Sep 14 13:55:37 2017 -0700
    Add pvalue and TSS distance for each eQTL. Input from Casey Brown, U Penn. refs #15646
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
  • lines changed 21, context: html, text, full: html, text
    6f4f71f60e9628b1e5887b5ed6099746292a142c Fri Sep 15 10:02:10 2017 -0700
    consistently used trackDb.gencode.ra for gencode track ra includes. This will lead to more automation
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 6, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV26lift37.ra
  • lines changed 1, context: html, text, full: html, text
    2468b0efbb0fbf5452e3c0b4f7874aca9298c98e Wed Sep 13 17:47:41 2017 -0700
    fixed crash in hgc due to attempting to use table that is not included in V26lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.html
  • lines changed 21, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.ra
  • lines changed 222, context: html, text, full: html, text
    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra
  • lines changed 7, context: html, text, full: html, text
    6f4f71f60e9628b1e5887b5ed6099746292a142c Fri Sep 15 10:02:10 2017 -0700
    consistently used trackDb.gencode.ra for gencode track ra includes. This will lead to more automation
• src/hg/makeDb/trackDb/human/hg38/gtexExpr.html
  • lines changed 108, context: html, text, full: html, text
    5f988c3d882a600f59a9dbcc9c1fdb6ca839d47b Mon Sep 11 13:26:41 2017 -0700
    Removing an unused HTML page now that hg38 and hg19 have a shared HTML page at the /human directory, refs #19350
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 18, context: html, text, full: html, text
    6f4f71f60e9628b1e5887b5ed6099746292a142c Fri Sep 15 10:02:10 2017 -0700
    consistently used trackDb.gencode.ra for gencode track ra includes. This will lead to more automation
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    54865dd4a5a0e78adc818a6f8c19c02cc21bc581 Mon Sep 11 15:48:10 2017 -0700
    Removing score filter for cosmic v82 tracks, all items have a score of 0. refs #19932
  • lines changed 15, context: html, text, full: html, text
    40a34c50eafab3d08708d91c765900d7231eeba2 Tue Sep 12 14:13:36 2017 -0700
    Making cosmic v82 track public, removing old v81 track, refs #19932
  • lines changed 9, context: html, text, full: html, text
    af9fd625f2b509b82fd1732c87648c322d5f5831 Thu Sep 14 15:46:46 2017 -0700
    Fixing ordering on hg38 variation group, refs #20100
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
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    6f4f71f60e9628b1e5887b5ed6099746292a142c Fri Sep 15 10:02:10 2017 -0700
    consistently used trackDb.gencode.ra for gencode track ra includes. This will lead to more automation
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.html
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    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
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    95aed5dee567f6a5422ea54d36fb2a0b3b93e1f4 Fri Sep 15 00:25:56 2017 -0700
    import of GENCODE V27lift37
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.ra
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    9c61e005e0f63c72e92173c9a5de54f06827fad4 Thu Sep 14 22:34:05 2017 -0700
    import of GENCODE V27
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
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    63287d454eb2a25f80ca208a9e02cab2909d631b Mon Sep 11 11:53:11 2017 -0700
    Removing release tags to release these tracks to the RR, refs #19350
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    33d5d6b4be90c9fa66a8845a5bdf9e0ef6039e41 Mon Sep 11 15:31:30 2017 -0700
    Updating the GTEx Gene Expression shortLabel now that the GTEx Transcript Expression track is now available, refs #19350
• src/hg/makeDb/trackDb/human/trackDb.ra
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    29f6438cff59bf1a4f99361742b71eb7bd1a1a25 Fri Sep 15 13:51:57 2017 -0700
    Staging SNPedia track on beta, refs #19811
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    f95f2a892de717c11a45f0600e9172cd1517d6f1 Fri Sep 15 17:38:47 2017 -0700
    trackDb changes for uniprot track, refs #19351
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    8a9f85529515309e935064aa2d53421978687dd7 Fri Sep 15 23:29:29 2017 -0700
    making snpedia a composite with two subtracks, refs #19811
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
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    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.html
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    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.ra
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    acb56f9b62903889ee721cdfef817093d3ec28b3 Fri Sep 15 09:52:55 2017 -0700
    load of GENCODE VM14; not being pushed
• src/hg/makeDb/trackDb/netCi2.html
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    767c3c3a6f1399d8ccf3d339d37597df04cbfe81 Tue Sep 12 08:55:08 2017 -0700
    Fixing broken links found by the broken link report for strPur2, no Redmine
• src/hg/makeDb/trackDb/netDm2.html
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    d0338a2e3f2038782eb35973d80b9ad93b6a1d2d Mon Sep 18 10:11:41 2017 -0700
    Fixing broken links found by the broken link report for droAna1, no Redmine
• src/hg/makeDb/trackDb/trackDb.ra
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    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
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    f95f2a892de717c11a45f0600e9172cd1517d6f1 Fri Sep 15 17:38:47 2017 -0700
    trackDb changes for uniprot track, refs #19351
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    b5ee047d7e951f39d1d2acd48df79febce07ef52 Fri Sep 15 17:40:25 2017 -0700
    fixing missing line in last commit
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    f95f2a892de717c11a45f0600e9172cd1517d6f1 Fri Sep 15 17:38:47 2017 -0700
    trackDb changes for uniprot track, refs #19351
• src/hg/makeDb/trackDb/uniprot.html
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    f95f2a892de717c11a45f0600e9172cd1517d6f1 Fri Sep 15 17:38:47 2017 -0700
    trackDb changes for uniprot track, refs #19351
• src/hg/utils/automation/HgAutomate.pm
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    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/hg/utils/automation/cluster.txt
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    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/hg/utils/automation/doNcbiRefSeq.pl
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    9accb12bf774a34a834ff1768434fc117433aec8 Fri Sep 15 15:17:54 2017 -0700
    Don't include 'other' items in fake PSL for ncbiRefSeq -- we need PSL only for accessioned transcripts.
• src/hg/utils/otto/uniprot/README.txt
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    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
• src/hg/utils/otto/uniprot/bed12UniProtAnnot.as
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    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
• src/hg/utils/otto/uniprot/doUniprot
  • lines changed 799, context: html, text, full: html, text
    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
  • lines changed 1, context: html, text, full: html, text
    8917ca0ff9a16f697d30b6b54effbd00fe112f9e Fri Sep 15 23:27:49 2017 -0700
    more uniprot changes, #19351
• src/hg/utils/otto/uniprot/makeUniProtPsl.sh
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    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/hg/utils/otto/uniprot/makefile
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    2220c7cd0175bc25a18d8ee38c7f9ae7487e3c60 Fri Sep 15 17:33:54 2017 -0700
    Major rewrite of the UniProt pipeline, many changes, refs #19351
• src/hg/utils/otto/uniprot/mapUniprot_doBlast
  • lines changed 18, context: html, text, full: html, text
    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/hg/utils/otto/uniprot/uniprotLift
  • lines changed 480, context: html, text, full: html, text
    8917ca0ff9a16f697d30b6b54effbd00fe112f9e Fri Sep 15 23:27:49 2017 -0700
    more uniprot changes, #19351
• src/hg/utils/uniprotMutations/makeUniProtToHg.sh
  • lines changed 59, context: html, text, full: html, text
    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/hg/utils/uniprotMutations/mapUniprot_doBlast
  • lines changed 18, context: html, text, full: html, text
    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    69149ba83d12c004221bade0c763cbb2531e2f6e Tue Sep 12 10:28:55 2017 -0700
    moving the cluster name from HgAutomate to a separate tiny text file, so it's easier to use from bash.
• src/utils/qa/weeklybld/buildEnv.csh
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    565f0400e16f85eca4c3e1b69858d84da3b189fb Mon Sep 18 10:48:47 2017 -0700
    v355 final build refs #20085

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• files changed: 122