File Changes for hiram

v440_preview2 to v440_base (2022-11-14 to 2022-11-21) v440

• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 33, context: html, text, full: html, text
    6d1c72eb5d13c0c9bd80170aa0131fd47d1edf90 Fri Nov 18 15:39:46 2022 -0800
    add discussion about how to make your track hub appear on a GenArk assembly hub refs #30297
  • lines changed 5, context: html, text, full: html, text
    5bfb5c9e786ed1a8c77b1d44a06a646831972b01 Fri Nov 18 15:43:53 2022 -0800
    add discussion about how to make your track hub appear on a GenArk assembly hub refs #30297
• src/hg/liftOver/tests/makefile
  • lines changed 27, context: html, text, full: html, text
    1cebb892646afdf2b2d01439a4921649835a850b Mon Nov 14 17:22:44 2022 -0800
    now using input files from URLs to hgdownload instead of local hgwdev files refs #29651
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 1, context: html, text, full: html, text
    71e09012455a01c07dd7953e16044361a287496a Fri Nov 18 13:59:00 2022 -0800
    now indicating chromAuthority ucsc on those browsers that can do that refs #30297
• src/hg/makeDb/doc/asmHubs/chromAuthority.pl
  • lines changed 100, context: html, text, full: html, text
    71e09012455a01c07dd7953e16044361a287496a Fri Nov 18 13:59:00 2022 -0800
    now indicating chromAuthority ucsc on those browsers that can do that refs #30297
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    1724db5437e3012b6bebf6229e3992b91923c53c Wed Nov 16 14:26:08 2022 -0800
    adding GCA_026108075.1_ASM2610807v1 green algae C.reinhardtii (CC-5816 2022) per user request refs #29545
  • lines changed 2350, context: html, text, full: html, text
    a606e7a02e51c2bc401392295d320950d7d72af1 Thu Nov 17 10:37:19 2022 -0800
    eliminate useless column 2 and clean up clade identifications refs #29545
  • lines changed 8, context: html, text, full: html, text
    8d241cb340c0a3a650ad3b8f3830ee150d780c02 Mon Nov 21 08:24:19 2022 -0800
    some potatos and Salmonella, hopefully not together, per user requests refs #29545
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 16, context: html, text, full: html, text
    71e09012455a01c07dd7953e16044361a287496a Fri Nov 18 13:59:00 2022 -0800
    now indicating chromAuthority ucsc on those browsers that can do that refs #30297
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8d241cb340c0a3a650ad3b8f3830ee150d780c02 Mon Nov 21 08:24:19 2022 -0800
    some potatos and Salmonella, hopefully not together, per user requests refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    40a599ef678220a659462c41c4d9fb9eda0db3d2 Fri Nov 18 15:03:19 2022 -0800
    adding a mouse assembly per user request refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1724db5437e3012b6bebf6229e3992b91923c53c Wed Nov 16 14:26:08 2022 -0800
    adding GCA_026108075.1_ASM2610807v1 green algae C.reinhardtii (CC-5816 2022) per user request refs #29545
  • lines changed 9, context: html, text, full: html, text
    f32381d3c31bcea401cda571ffef89c2bd9786d4 Fri Nov 18 14:14:39 2022 -0800
    adding some potato assemblies per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    8d241cb340c0a3a650ad3b8f3830ee150d780c02 Mon Nov 21 08:24:19 2022 -0800
    some potatos and Salmonella, hopefully not together, per user requests refs #29545
• src/lib/pipeline.c
  • lines changed 5, context: html, text, full: html, text
    470c5c8fc13a81b0424a46ed3f4686ca8a703a0f Wed Nov 16 15:43:37 2022 -0800
    fix error in sysconf return on Mac OSX M1/arm64 machine refs #29651
• src/utils/findMotif/findMotif.c
  • lines changed 60, context: html, text, full: html, text
    c51d3a655973d0b9ee21f0ab1ff5b657f89c6893 Mon Nov 14 23:32:31 2022 -0800
    now using a universal popcnt "library" to avoid any machine architecture differences refs @29651
• src/utils/findMotif/libpopcnt.h
  • lines changed 798, context: html, text, full: html, text
    c51d3a655973d0b9ee21f0ab1ff5b657f89c6893 Mon Nov 14 23:32:31 2022 -0800
    now using a universal popcnt "library" to avoid any machine architecture differences refs @29651
• src/utils/findMotif/makefile
  • lines changed 1, context: html, text, full: html, text
    c51d3a655973d0b9ee21f0ab1ff5b657f89c6893 Mon Nov 14 23:32:31 2022 -0800
    now using a universal popcnt "library" to avoid any machine architecture differences refs @29651
• src/utils/findMotif/tests/expected/test10.txt.gz
  • lines changed 0, context: html, text, full: html, text
    c51d3a655973d0b9ee21f0ab1ff5b657f89c6893 Mon Nov 14 23:32:31 2022 -0800
    now using a universal popcnt "library" to avoid any machine architecture differences refs @29651
• src/utils/findMotif/tests/expected/test9.txt.gz
  • lines changed 0, context: html, text, full: html, text
    c51d3a655973d0b9ee21f0ab1ff5b657f89c6893 Mon Nov 14 23:32:31 2022 -0800
    now using a universal popcnt "library" to avoid any machine architecture differences refs @29651
• src/utils/findMotif/tests/makefile
  • lines changed 30, context: html, text, full: html, text
    67eca6b636d365e436b5aa1bcba7316fd60d27aa Mon Nov 14 22:45:24 2022 -0800
    generic makefile to function on linux and in Mac OSX environment refs #29651
• src/utils/makefile
  • lines changed 6, context: html, text, full: html, text
    6bc9515bd7543f451b7d03264f051a020128fb80 Mon Nov 14 23:59:41 2022 -0800
    findMotif now has a universal popcnt "library" to avoid any machine architecture differences refs @29651