File Changes for hiram

v443_base to v444_preview (2023-01-30 to 2023-02-06) v444

• src/hg/gar/rebuild.sh
  • lines changed 9, context: html, text, full: html, text
    eea1ea7511ae244feb7c92616d0d463896dc851d Thu Feb 2 13:22:59 2023 -0800
    send assemblyTable and requestTable listings out to hgdownload no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    8ee7c8aa28f59334f4a99f7dbe8395bf884a4886 Tue Jan 31 10:32:08 2023 -0800
    adding GCA_000300575.2_ASM30057v2 basidiomycete A.bisporus (H97 2016) per user request refs #29545
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    f2a57847f1a0a95ccaac0f31f79b1438cfee7452 Wed Feb 1 15:11:12 2023 -0800
    add the California mussel for the CCGP project no redmine
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    ff9640d3cacadb3a108731e806a471d6d69ca293 Thu Feb 2 14:25:03 2023 -0800
    adding in some CCGP genome builds no redmine
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
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    f066a3c7e3410f07595c5039b285f79da29c09c5 Thu Feb 2 14:48:01 2023 -0800
    adding some assemblies to CCGP no redmine
• src/hg/makeDb/doc/ccgpAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
• src/hg/makeDb/doc/ccgpAsmHub/makefile
  • lines changed 23, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8ee7c8aa28f59334f4a99f7dbe8395bf884a4886 Tue Jan 31 10:32:08 2023 -0800
    adding GCA_000300575.2_ASM30057v2 basidiomycete A.bisporus (H97 2016) per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f2a57847f1a0a95ccaac0f31f79b1438cfee7452 Wed Feb 1 15:11:12 2023 -0800
    add the California mussel for the CCGP project no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 6, context: html, text, full: html, text
    a3681e7888030cebc1023f74d77158862dd39a51 Tue Jan 31 11:45:57 2023 -0800
    catching up a number of recent additions no redmine
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    2dd607cbec07de1fe0ccf93b835fd19bcb147d76 Tue Jan 31 11:48:33 2023 -0800
    the extra one GCA_009914755.4_T2T-CHM13v2.0 is required since it is artifically added no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    e3f062b5aadf38361ca54bd25b6604bd5610dad8 Tue Jan 31 10:33:50 2023 -0800
    the GRCh38 versions are now legacy so as not to compete with hg38.p14 and a fungus has become obsolete per user request refs #29545
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 1, context: html, text, full: html, text
    21f4b0da7fe6f8d64ba6d67cabb4bb464df44112 Tue Jan 31 12:21:53 2023 -0800
    correct symlink to ../trackData/ not to ../trackDb/ no redmine
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 6, context: html, text, full: html, text
    960327879cd684b279610a26bcd311625c401b02 Tue Jan 31 11:17:32 2023 -0800
    incorrect buildDir variable in the netSyntenic step fixed no redmine
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 6, context: html, text, full: html, text
    5f82f3c44e6e68741fde81a878958cad5d327c6e Tue Jan 31 11:24:48 2023 -0800
    incorrect buildDir variable in the loadRBest step fixed no redmine
• src/hg/utils/otto/genArk/genArkListToSql.pl
  • lines changed 44, context: html, text, full: html, text
    c4c80a07b85c6aa44fa6f862536e297c8310a53a Thu Feb 2 12:37:12 2023 -0800
    adding otto cron scripts to keep the hgcentral.genark table up to date
• src/hg/utils/otto/genArk/updateHgcentral.sh
  • lines changed 113, context: html, text, full: html, text
    c4c80a07b85c6aa44fa6f862536e297c8310a53a Thu Feb 2 12:37:12 2023 -0800
    adding otto cron scripts to keep the hgcentral.genark table up to date
  • lines changed 11, context: html, text, full: html, text
    70124b0bcc90d53de666f37cccd6b1a4356161de Thu Feb 2 12:45:54 2023 -0800
    correctly check for an unbound variable no redmine
• src/hg/utils/otto/otto.crontab
  • lines changed 7, context: html, text, full: html, text
    105fed4179457f1d6ae6fb3daa94cd0cd0270451 Thu Feb 2 12:48:45 2023 -0800
    catch up with current crontab in otto user no redmine
  • lines changed 1, context: html, text, full: html, text
    230381336761678f15ec2bb28751ce9d558fbd3c Thu Feb 2 12:52:08 2023 -0800
    restore Lou's edit of 03 Jan to reduce frequency of lrgWrapper no redmine
  • lines changed 4, context: html, text, full: html, text
    2a1eb01eec5310638a682d97ef6e6e0204062bca Thu Feb 2 12:59:26 2023 -0800
    adding GenArk updating hgcentral.genark table once a week no redmine