All File Changes

v393_preview2 to v393_base (2020-01-20 to 2020-01-27) v393

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    f6c1c36a3ab903529fc5855bf3de785434b4cad7 Fri Jan 24 15:15:22 2020 -0800
    Increment BLAT version. This makes it easier to do the gfServer rollout. Now we can easily identify the newest versions that tolerate IPv6 being disabled.
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 51, context: html, text, full: html, text
    b045a054fe063e155ecc27327079cf62a53ff63b Fri Jan 17 14:03:13 2020 -0800
    Deleting psychic, adding UCSC Cell Atlas refs #23930 #23931
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 10, context: html, text, full: html, text
    ba14f4302cf8fb07c94849c27fe1793ddabdbc92 Tue Jan 21 12:17:09 2020 -0800
    Adding track height URL setting #24794
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 2, context: html, text, full: html, text
    3a5369a02eabb119a6265910fda1ad76be3cba5f Fri Jan 24 11:48:14 2020 -0800
    adding hyphen
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 8, context: html, text, full: html, text
    ba14f4302cf8fb07c94849c27fe1793ddabdbc92 Tue Jan 21 12:17:09 2020 -0800
    Adding track height URL setting #24794
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 12, context: html, text, full: html, text
    9b46c8ee5e9bc0dfd758600b92402d7e09155c01 Wed Jan 22 15:27:27 2020 -0800
    Adding a hint about group auto-scale setting being adjustable in terms of opting out subtracks in a composite refs #24770
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 28, context: html, text, full: html, text
    e45b31facc4d22170d23baa9016bfb82de3c55c1 Fri Jan 24 13:01:44 2020 -0800
    Revising superTrack visibility explanations requested by Max refs #24746
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 13, context: html, text, full: html, text
    97592d3ab7dc59115a7f0c434776cbe823acf818 Wed Jan 22 11:54:21 2020 -0800
    Updating the query.html examples to match the new RefSeq accessions on dev, not needing pushing out until the push of the new accessions refs #24808
  • lines changed 1, context: html, text, full: html, text
    500dee92610ffa5c31fad913639375852e6de6af Wed Jan 22 12:13:04 2020 -0800
    Updating the query.html with new HGVS accessions refs #24808
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    2754dfae7628e479013cdf2bb2c7d1416458a4f9 Thu Jan 23 17:10:52 2020 -0800
    Adding examples of superTrack visibility and more verbose explanations requested by Max refs #24746
  • lines changed 1, context: html, text, full: html, text
    e45b31facc4d22170d23baa9016bfb82de3c55c1 Fri Jan 24 13:01:44 2020 -0800
    Revising superTrack visibility explanations requested by Max refs #24746
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 3, context: html, text, full: html, text
    2754dfae7628e479013cdf2bb2c7d1416458a4f9 Thu Jan 23 17:10:52 2020 -0800
    Adding examples of superTrack visibility and more verbose explanations requested by Max refs #24746
  • lines changed 2, context: html, text, full: html, text
    e45b31facc4d22170d23baa9016bfb82de3c55c1 Fri Jan 24 13:01:44 2020 -0800
    Revising superTrack visibility explanations requested by Max refs #24746
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 116, context: html, text, full: html, text
    2754dfae7628e479013cdf2bb2c7d1416458a4f9 Thu Jan 23 17:10:52 2020 -0800
    Adding examples of superTrack visibility and more verbose explanations requested by Max refs #24746
  • lines changed 90, context: html, text, full: html, text
    e45b31facc4d22170d23baa9016bfb82de3c55c1 Fri Jan 24 13:01:44 2020 -0800
    Revising superTrack visibility explanations requested by Max refs #24746
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 26, context: html, text, full: html, text
    125b79e5c4908d8c0015c53e16db2003dd02a7c5 Mon Jan 20 17:05:33 2020 -0800
    Announcing the 1000 Genomes Project variants track for hg38, refs #21805
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    125b79e5c4908d8c0015c53e16db2003dd02a7c5 Mon Jan 20 17:05:33 2020 -0800
    Announcing the 1000 Genomes Project variants track for hg38, refs #21805
• src/hg/htdocs/staff.html
  • lines changed 8, context: html, text, full: html, text
    8a033b30af2bf82ac31af16a3e5112ea08ca12fd Wed Jan 22 14:41:33 2020 -0800
    Moving Conner and ChrisV into alumni on staff page
• src/hg/htdocs/training/index.html
  • lines changed 6, context: html, text, full: html, text
    ae8c567e5f1b93dc0f2ad1bdd61600d7bcd3a956 Tue Jan 21 15:34:43 2020 -0800
    added link to UHSU workshop
  • lines changed 11, context: html, text, full: html, text
    ace96f644f2c0f1477594723218546ffe0c93137 Mon Jan 27 09:23:06 2020 -0800
    added link to ucsf workshop. activted Nijmegen mention now that confirmed
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    b412374f3148d14f102d1173a845781eab27d39e Mon Jan 27 10:09:59 2020 -0800
    New version number v393
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 44, context: html, text, full: html, text
    06c02db4f03372ffd0d386846d4d9de377a36555 Wed Jan 22 14:24:30 2020 -0800
    getting the build system for assembly hubs into a single set of files for all categories of hubs refs #24812
  • lines changed 13, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
• src/hg/makeDb/doc/asmHubs/birds.asmId.commonName.tsv
  • lines changed 65, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/birds.commonName.asmId.orderList.tsv
  • lines changed 65, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/fish.asmId.commonName.tsv
  • lines changed 76, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/fish.commonName.asmId.orderList.tsv
  • lines changed 76, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/groups.txt
  • lines changed 39, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
• src/hg/makeDb/doc/asmHubs/mammals.asmId.commonName.tsv
  • lines changed 107, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/mammals.commonName.asmId.orderList.tsv
  • lines changed 107, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 292, context: html, text, full: html, text
    06c02db4f03372ffd0d386846d4d9de377a36555 Wed Jan 22 14:24:30 2020 -0800
    getting the build system for assembly hubs into a single set of files for all categories of hubs refs #24812
  • lines changed 6, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
  • lines changed 10, context: html, text, full: html, text
    cdd0101336b3399e8d1a204a298b017a2675cc3a Fri Jan 24 10:35:41 2020 -0800
    now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 191, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
  • lines changed 4, context: html, text, full: html, text
    cdd0101336b3399e8d1a204a298b017a2675cc3a Fri Jan 24 10:35:41 2020 -0800
    now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 261, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
  • lines changed 7, context: html, text, full: html, text
    cdd0101336b3399e8d1a204a298b017a2675cc3a Fri Jan 24 10:35:41 2020 -0800
    now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 90, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
  • lines changed 3, context: html, text, full: html, text
    cdd0101336b3399e8d1a204a298b017a2675cc3a Fri Jan 24 10:35:41 2020 -0800
    now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748
• src/hg/makeDb/doc/asmHubs/primates.asmId.commonName.tsv
  • lines changed 23, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
• src/hg/makeDb/doc/asmHubs/primates.commonName.asmId.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    6c8734919a8bbcc7b0ef17a89ef86d21d80686cb Thu Jan 23 14:25:13 2020 -0800
    now using a minimal makefile and common scripts to make any assembly hub refs #24748
• src/hg/makeDb/doc/asmHubs/vertebrate.asmId.commonName.tsv
  • lines changed 25, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/asmHubs/vertebrate.commonName.asmId.orderList.tsv
  • lines changed 25, context: html, text, full: html, text
    ca0ca22adfb11121eb55173b00b4b7ccca8f8483 Fri Jan 24 10:33:49 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/birdsAsmHub/birds.taxId.list
  • lines changed 73, context: html, text, full: html, text
    6f4846b142aee32ea1fe219d37516d6ed5c8e4e4 Fri Jan 24 10:23:29 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/birdsAsmHub/birds.xrefName.list
  • lines changed 65, context: html, text, full: html, text
    6f4846b142aee32ea1fe219d37516d6ed5c8e4e4 Fri Jan 24 10:23:29 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/birdsAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    6f4846b142aee32ea1fe219d37516d6ed5c8e4e4 Fri Jan 24 10:23:29 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/birdsAsmHub/makefile
  • lines changed 8, context: html, text, full: html, text
    6f4846b142aee32ea1fe219d37516d6ed5c8e4e4 Fri Jan 24 10:23:29 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/birdsAsmHub/mkList.sh
  • lines changed 28, context: html, text, full: html, text
    6f4846b142aee32ea1fe219d37516d6ed5c8e4e4 Fri Jan 24 10:23:29 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/fishAsmHub/fish.taxId.list
  • lines changed 76, context: html, text, full: html, text
    4168dd3ec951fda1bf8a881bae03cb82de890a2d Fri Jan 24 10:21:51 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/fishAsmHub/fish.xrefName.list
  • lines changed 76, context: html, text, full: html, text
    4168dd3ec951fda1bf8a881bae03cb82de890a2d Fri Jan 24 10:21:51 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/fishAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    4168dd3ec951fda1bf8a881bae03cb82de890a2d Fri Jan 24 10:21:51 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/fishAsmHub/makefile
  • lines changed 8, context: html, text, full: html, text
    4168dd3ec951fda1bf8a881bae03cb82de890a2d Fri Jan 24 10:21:51 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/fishAsmHub/mkList.sh
  • lines changed 30, context: html, text, full: html, text
    4168dd3ec951fda1bf8a881bae03cb82de890a2d Fri Jan 24 10:21:51 2020 -0800
    now using the minimal makefile procedure with common scripts refs #24748
• src/hg/makeDb/doc/globalReference/commonNameOrder.list
  • lines changed 1, context: html, text, full: html, text
    e03deb26dffb5889987cfc141f59fdc27fc9d284 Mon Jan 20 16:16:00 2020 -0800
    Fixing typo in Bangladesh #24354
• src/hg/makeDb/doc/globalReference/commonNames.txt
  • lines changed 1, context: html, text, full: html, text
    e03deb26dffb5889987cfc141f59fdc27fc9d284 Mon Jan 20 16:16:00 2020 -0800
    Fixing typo in Bangladesh #24354
• src/hg/makeDb/doc/globalReference/ethnicGroup.txt
  • lines changed 1, context: html, text, full: html, text
    7690db59c94f7a49856aa3ee5eb7edf496976f21 Mon Jan 20 15:29:06 2020 -0800
    Fixing spelling of Bangladesh #24354
• src/hg/makeDb/doc/globalReference/family.txt
  • lines changed 1, context: html, text, full: html, text
    e03deb26dffb5889987cfc141f59fdc27fc9d284 Mon Jan 20 16:16:00 2020 -0800
    Fixing typo in Bangladesh #24354
• src/hg/makeDb/doc/globalReference/hub.txt
  • lines changed 2, context: html, text, full: html, text
    e03deb26dffb5889987cfc141f59fdc27fc9d284 Mon Jan 20 16:16:00 2020 -0800
    Fixing typo in Bangladesh #24354
• src/hg/makeDb/doc/globalReference/mkSymLinks.sh
  • lines changed 3, context: html, text, full: html, text
    8a407abcc7db4a11459d510159866c30628500d6 Fri Jan 24 09:54:25 2020 -0800
    do not make symlinks to jpg files, there are none refs #24354
• src/hg/makeDb/doc/hg19.addChrMT.txt
  • lines changed 446, context: html, text, full: html, text
    704efd7a1be11b0d69aff4a9101f87ed5b62734d Thu Jan 23 10:10:10 2020 -0800
    Add NC_012920 (rCRS) mitochondrion to hg19 as chrMT. refs #24648
• src/hg/makeDb/doc/hg19.patchUpdate.13.txt
  • lines changed 11, context: html, text, full: html, text
    704efd7a1be11b0d69aff4a9101f87ed5b62734d Thu Jan 23 10:10:10 2020 -0800
    Add NC_012920 (rCRS) mitochondrion to hg19 as chrMT. refs #24648
• src/hg/makeDb/doc/hg19.txt
  • lines changed 32, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
  • lines changed 13, context: html, text, full: html, text
    30308acabd47a5ba91516d88ee303ef0e3853f55 Tue Jan 21 19:11:12 2020 -0800
    load GENCODE V19 MT sequences to chrMT
  • lines changed 4, context: html, text, full: html, text
    704efd7a1be11b0d69aff4a9101f87ed5b62734d Thu Jan 23 10:10:10 2020 -0800
    Add NC_012920 (rCRS) mitochondrion to hg19 as chrMT. refs #24648
• src/hg/makeDb/doc/mammalsAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    bc11548eb5339314793227ba341d159a258095de Thu Jan 23 15:19:50 2020 -0800
    now using minimal makefile and common script to construct index pages refs #24748
• src/hg/makeDb/doc/mammalsAsmHub/makefile
  • lines changed 6, context: html, text, full: html, text
    bc11548eb5339314793227ba341d159a258095de Thu Jan 23 15:19:50 2020 -0800
    now using minimal makefile and common script to construct index pages refs #24748
• src/hg/makeDb/doc/mammalsAsmHub/mammals.taxId.list
  • lines changed 104, context: html, text, full: html, text
    bf997eaafa35943b83c54e8a31e5077792b69b50 Fri Jan 24 10:30:03 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/mammalsAsmHub/mammals.xrefName.list
  • lines changed 107, context: html, text, full: html, text
    bf997eaafa35943b83c54e8a31e5077792b69b50 Fri Jan 24 10:30:03 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/mammalsAsmHub/mkList.sh
  • lines changed 39, context: html, text, full: html, text
    bc11548eb5339314793227ba341d159a258095de Thu Jan 23 15:19:50 2020 -0800
    now using minimal makefile and common script to construct index pages refs #24748
• src/hg/makeDb/doc/primateAsmHub/groups.txt
  • lines changed 39, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/hub.txt
  • lines changed 1, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 6, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/makefile
  • lines changed 5, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 39, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/mkAsmStats.pl
  • lines changed 11, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 259, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl
  • lines changed 59, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 182, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl
  • lines changed 32, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 244, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/mkList.sh
  • lines changed 25, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/mkSymLinks.pl
  • lines changed 46, context: html, text, full: html, text
    19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b Tue Jan 21 13:22:47 2020 -0800
    now using new style GCF path names and separate hubs for each assembly refs #24748
  • lines changed 180, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/primates.asmId.commonName.tsv
  • lines changed 23, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primateAsmHub/primates.commonName.asmId.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    a7652d074beefd4f023287d09ec32bc2bbf43796 Fri Jan 24 10:26:32 2020 -0800
    now using common scripts to build hubs refs #24748
• src/hg/makeDb/doc/primatesAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    9c97ac4e5ef2fb2b6ef04470ba798e0d87e5c1ce Thu Jan 23 14:23:12 2020 -0800
    now using a minimal makefile to make assembly hub index page and symlinks refs #24748
• src/hg/makeDb/doc/primatesAsmHub/makefile
  • lines changed 6, context: html, text, full: html, text
    9c97ac4e5ef2fb2b6ef04470ba798e0d87e5c1ce Thu Jan 23 14:23:12 2020 -0800
    now using a minimal makefile to make assembly hub index page and symlinks refs #24748
• src/hg/makeDb/doc/primatesAsmHub/mkList.sh
  • lines changed 25, context: html, text, full: html, text
    9c97ac4e5ef2fb2b6ef04470ba798e0d87e5c1ce Thu Jan 23 14:23:12 2020 -0800
    now using a minimal makefile to make assembly hub index page and symlinks refs #24748
• src/hg/makeDb/doc/primatesAsmHub/primates.taxId.list
  • lines changed 26, context: html, text, full: html, text
    d692906ff30b46e32e7634fae0865ab40d1bc557 Fri Jan 24 10:28:44 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/primatesAsmHub/primates.xrefName.list
  • lines changed 23, context: html, text, full: html, text
    d692906ff30b46e32e7634fae0865ab40d1bc557 Fri Jan 24 10:28:44 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/groups.txt
  • lines changed 39, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 39, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
• src/hg/makeDb/doc/vertebratesAsmHub/makefile
  • lines changed 39, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 34, context: html, text, full: html, text
    831f64579844a0fbd41935fc844160991d44dbb0 Thu Jan 23 15:28:33 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/mkAsmStats.pl
  • lines changed 262, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 262, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl
  • lines changed 182, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 182, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl
  • lines changed 241, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 241, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/mkList.sh
  • lines changed 28, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 2, context: html, text, full: html, text
    831f64579844a0fbd41935fc844160991d44dbb0 Thu Jan 23 15:28:33 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl
  • lines changed 180, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 180, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.asmId.commonName.tsv
  • lines changed 25, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 25, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.commonName.asmId.orderList.tsv
  • lines changed 25, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 25, context: html, text, full: html, text
    026fea8dd26483276dbc4d8c860ff0d11e1a640e Thu Jan 23 15:27:43 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.taxId.list
  • lines changed 29, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 29, context: html, text, full: html, text
    9ad283f7e22efeee51bd4b183582827082494117 Thu Jan 23 15:28:14 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
  • lines changed 29, context: html, text, full: html, text
    48a02b14618de832751fb89174fceaaf64becb29 Fri Jan 24 10:30:46 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/doc/vertebratesAsmHub/vertebrate.xrefName.list
  • lines changed 26, context: html, text, full: html, text
    f654134d5172e2687b3e6f98da7db78dd8379387 Tue Jan 21 15:01:57 2020 -0800
    initial set of files to build "other vertebrates" assembly hub refs #2482
  • lines changed 26, context: html, text, full: html, text
    9ad283f7e22efeee51bd4b183582827082494117 Thu Jan 23 15:28:14 2020 -0800
    now using new minimal makefile with single set of scripts refs #24748
  • lines changed 26, context: html, text, full: html, text
    48a02b14618de832751fb89174fceaaf64becb29 Fri Jan 24 10:30:46 2020 -0800
    record outputs from mkList.sh refs #24748
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    b48c99362efd8106198ec7eda17b68ce74ec6acc Thu Jan 23 14:31:28 2020 -0800
    Add Gidget to genbank species list
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 6, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 91, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/trackDb/clinvarLift.html
  • lines changed 99, context: html, text, full: html, text
    a1cbac0f4ffff0ec3f9f709e48ef04fcc9769aa3 Fri Jan 24 08:00:44 2020 -0800
    adding a do script for clinvar lift track and docs page, refs #24825 (Not sure what to do about makedocs for an automated track like this)
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 22, context: html, text, full: html, text
    4292df2e620ca7e3bdad1a0a7ba10a392aa9c5cb Thu Jan 23 13:29:49 2020 -0800
    Adding Data Access section to GTEx page #24826
  • lines changed 32, context: html, text, full: html, text
    51bc9725be0e2110befd07389bf7287f0ce7c256 Fri Jan 24 17:10:07 2020 -0800
    Adding more info to the Data Access section to GTEx page refs #24826
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 2, context: html, text, full: html, text
    dedc44398c7af029c502233b977566cfbcfcc340 Fri Jan 24 08:31:16 2020 -0800
    Forgot to add a release tag to the new bigBed dgv track, which caused the track to go missing on the RR because the bigDataUrl didn't exist
  • lines changed 1, context: html, text, full: html, text
    6f75f44f9a88552231f44f488c15bfe7cfc89229 Fri Jan 24 09:24:04 2020 -0800
    One more fix to get dgvMerged back
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV33lift37.html
  • lines changed 32, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV33lift37.ra
  • lines changed 224, context: html, text, full: html, text
    12a7062ec0510b37e2cb6e8c294b53d2b0af69e0 Tue Jan 21 18:24:46 2020 -0800
    import of gencodeV33lift37
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    645d4868cc3a43a141e466672a4d5ac9ae0c1208 Mon Jan 20 17:19:15 2020 -0800
    Adding the pennantIcon for the 1000 Genomes Project variant track for hg38, refs #21805
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 5, context: html, text, full: html, text
    b5b1ff3206f46b137026b38b6f199073cf3c1977 Fri Jan 24 17:02:06 2020 -0800
    made curated and submitted more obvious in description. added mention of use of teh word Coverage. Per Ana Benet. Refs #24817
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    bb71cc8b992ac73246b27228cfa31317754b0299 Fri Jan 24 16:40:09 2020 -0800
    rationalized groups and nomenclature to CNV classes. Simplified selection matrix. Per Ana Benet. Refs #24817
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 8, context: html, text, full: html, text
    329ef2e1f93ff5e7c00ffdf3b5fe97e65a86a066 Fri Jan 24 05:33:54 2020 -0800
    improving RefSeq Select docs, refs #24787
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    eff3e5db3801d1f516a3230d6f106bc89a6e0db9 Thu Jan 23 08:03:02 2020 -0800
    adding clinvar lift track, right now only for pig, refs #24825
  • lines changed 5, context: html, text, full: html, text
    a1cbac0f4ffff0ec3f9f709e48ef04fcc9769aa3 Fri Jan 24 08:00:44 2020 -0800
    adding a do script for clinvar lift track and docs page, refs #24825 (Not sure what to do about makedocs for an automated track like this)
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 39, context: html, text, full: html, text
    a4b95829492ef38feb9369fecd8a0451d35c4103 Tue Jan 21 13:21:23 2020 -0800
    now using the new style GCF path names refs #24748
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 24, context: html, text, full: html, text
    2c31dc19ba22fc34ecc65c292bfb3badf12ca7ca Thu Jan 23 14:17:34 2020 -0800
    now adding ncbiRefSeqSelectCurated track refs #24748
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 2, context: html, text, full: html, text
    9d57b3048d4df5f3164f1a3f56f36a0d1f700e34 Thu Jan 23 11:02:36 2020 -0800
    need to have asmId.faSize.txt in top level directory for asmHubStats refs #24748
  • lines changed 1, context: html, text, full: html, text
    e828b8c24fd241d8a974cc4d5bbccbebc9de89de Thu Jan 23 15:10:59 2020 -0800
    use warnOnly on the gff conversion in ncbiRefSeq track refs #24748
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 34, context: html, text, full: html, text
    51d2baad200a4ef6f339fc30ec67444117153e1e Thu Jan 23 14:18:21 2020 -0800
    now adding ncbiRefSeqSelectCurated track refs #24748
  • lines changed 7, context: html, text, full: html, text
    c43865d1c59800b4e4a72c9a334e51b5e103e385 Thu Jan 23 15:11:51 2020 -0800
    correctly ignore failure to find MANE or select genes refs #24748
• src/hg/utils/automation/findEnsFtpNames.sh
  • lines changed 14, context: html, text, full: html, text
    b1b2e5b7727c19291acb605ad561dfbd225b0496 Tue Jan 21 10:30:24 2020 -0800
    cleaning up some errors for Ensembl v99 build no redmine
• src/hg/utils/hubCheck/tests/input/supertrackChild.txt
  • lines changed 97, context: html, text, full: html, text
    fd51b6d8f404ab7208683c3a58f95cfcac3f3f4f Fri Jan 24 08:42:24 2020 -0800
    adding supertrack test case to hubCheck tests, refs #13428#note-62
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    fd51b6d8f404ab7208683c3a58f95cfcac3f3f4f Fri Jan 24 08:42:24 2020 -0800
    adding supertrack test case to hubCheck tests, refs #13428#note-62
• src/hg/utils/hubClone/hubClone.c
  • lines changed 81, context: html, text, full: html, text
    32514d2022bc8c424480258e3a138c70eff3a48b Fri Jan 24 15:48:55 2020 -0800
    Adding command line option to download track hub data files to hubClone, refs #24835
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    f6c1c36a3ab903529fc5855bf3de785434b4cad7 Fri Jan 24 15:15:22 2020 -0800
    Increment BLAT version. This makes it easier to do the gfServer rollout. Now we can easily identify the newest versions that tolerate IPv6 being disabled.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    b412374f3148d14f102d1173a845781eab27d39e Mon Jan 27 10:09:59 2020 -0800
    New version number v393
• src/utils/doClinvarLift
  • lines changed 46, context: html, text, full: html, text
    a1cbac0f4ffff0ec3f9f709e48ef04fcc9769aa3 Fri Jan 24 08:00:44 2020 -0800
    adding a do script for clinvar lift track and docs page, refs #24825 (Not sure what to do about makedocs for an automated track like this)
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    dffe0bb6701e0637bf510bb07dc3116f6482eae5 Mon Jan 27 10:02:28 2020 -0800
    v393 final build, refs #24777

• lines changed: 7476
• files changed: 147