Commits for hiram

v437_base to v438_preview (2022-09-19 to 2022-09-26) v438

afe1592acd7a4dd79f8ca81b390d10113cb6aadc Tue Sep 20 09:40:42 2022 -0700

• more complete accounting of all GenArk and UCSC assemblies to get them into the page refs #28930
  • src/hg/gar/garTable.pl - lines changed 116, context: html, text, full: html, text
  • src/hg/gar/garTable.sh - lines changed 5, context: html, text, full: html, text

ca81b42b47cd5b6419d87f3b8697a0806ce85e99 Tue Sep 20 11:45:40 2022 -0700

• see if the referer and referDomain can be recorded for possible protection refs #28930
  • src/hg/gar/gar.cgi.pl - lines changed 18, context: html, text, full: html, text

dc7e4fa869733e45e0abdb1f2b9e4508ef7b802a Tue Sep 20 12:10:34 2022 -0700

• correct bioRxiv reference for the paper in preprint status refs #29982
  • src/hg/makeDb/trackDb/TOGAannotation.html - lines changed 3, context: html, text, full: html, text

3a278e49fbd9fcfcd01d427e68c5a14d85f9be6d Wed Sep 21 10:34:29 2022 -0700

• done with mpxv2022 experiment
  • src/hg/makeDb/trackDb/virus/mpxv2022/assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/chainNet.html - lines changed 148, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/cpgIslands.html - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/description.html - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/ncbiGene.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/pcrAmplicon.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/repeatMasker.html - lines changed 261, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/tanDups.html - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/trackDb.ra - lines changed 204, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/mpxv2022/windowMasker.html - lines changed 38, context: html, text, full: html, text

ac38533f23605cb72cffcf3017838c9a10dab63e Wed Sep 21 16:06:17 2022 -0700

• now making a track for TOGA annotations refs #29982
  • src/hg/utils/automation/asmHubTOGA.pl - lines changed 184, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 52, context: html, text, full: html, text

86fd61c5e8efe6d7ac42baa32b891fc1cf9e61bf Thu Sep 22 13:57:04 2022 -0700

• add the option of using a customNames.tsv file to add arbitrary listings refs #29982
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 21, context: html, text, full: html, text

6c04b75f3169885273b9979eb5a00e7841e1600f Sat Sep 24 14:57:58 2022 -0700

• correct the assembly name of GCF_016700215.2 no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

a529cabbe6ecc9e1dc9a9321bdfdcc6db1d10318 Sat Sep 24 15:18:10 2022 -0700

• default vis pack for TOGA track refs #29982
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 2, context: html, text, full: html, text

98a8fb9dfe585027839a944b73cb84f0a244f0ae Sat Sep 24 18:36:17 2022 -0700

• adding custom category to handle TOGA name changes refs #29982
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 2, context: html, text, full: html, text

e0232de768e8056705fd15b8bf908d99d3ea74e8 Sat Sep 24 18:37:56 2022 -0700

• do not fill in names for RefSeq or GenBank if either of those is not defined refs #29982
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 26, context: html, text, full: html, text

980db7f979bf44931256f421017262d2983f6aa1 Sat Sep 24 18:39:43 2022 -0700

• correct blank line after output and get queryDate and queryAsmName up a level so they can be used in all sections refs #29982
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 12, context: html, text, full: html, text

7f54f5b04dd45175af6af8ed3d7095c1aefa22b2 Sat Sep 24 18:41:55 2022 -0700

• correctly using dbHost in place of hgwdev refs #29982
  • src/hg/utils/automation/asmHubChainNetComposite.pl - lines changed 1, context: html, text, full: html, text

adbcbc19d8a90533fc04a2c6a164786fd10e945b Sat Sep 24 18:42:41 2022 -0700

• and yet one final name change for T2T-CHM13 refs @29982
  • src/hg/utils/automation/HgAutomate.pm - lines changed 1, context: html, text, full: html, text