Commits for hiram

v429_base to v430_preview (2022-04-04 to 2022-04-11) v430

257a178f6045d49ab8051fc298a2d021bec6790b Tue Apr 5 11:13:21 2022 -0700

• adding liftOver tracks changing organism name adding otherAligners directory and fasta.fa.gz download refs #29207
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 8, context: html, text, full: html, text

9eb815896a25137c6c784c5860c432b10d0d9964 Tue Apr 5 11:15:32 2022 -0700

• adding HG002 mat and pat builds and Macaca_fascicularis_6.0 refs #29207
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text

90555f803fa25829e2bf91e2faa913433999896f Tue Apr 5 11:16:39 2022 -0700

• new style chromAlias refs #29109
  • src/hg/utils/automation/asmHubChromAlias.pl - lines changed 72, context: html, text, full: html, text

8d2de5d51f2b37ece3f733c5a575b3c74bb2c8e6 Tue Apr 5 11:18:00 2022 -0700

• more meta data on the query and target for later use in doc construction refs #29207
  • src/hg/utils/automation/pairLastz.sh - lines changed 27, context: html, text, full: html, text

968f93baf48b914f5b7d127e68a5228dad673118 Tue Apr 5 11:20:08 2022 -0700

• adding in liftOver chainNet definitions refs #29207
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 112, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 68, context: html, text, full: html, text

fa292e61ad7da9d9ac6507b19835b88eec89e85c Tue Apr 5 14:08:07 2022 -0700

• catch up some mammal run statements that had been overlooked refs #29207
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text

3d8b609d2c0ef12c790e1564ad76989cc19c0c0d Tue Apr 5 22:07:06 2022 -0700

• adding the human chainNet composite refs #29207
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text

41ab5fa75567827d1b4141f9f352b0fc63922cee Tue Apr 5 23:09:19 2022 -0700

• priority ordering on the chain and net tracks refs #28907
  • src/hg/makeDb/trackDb/human/chainNetHuman.ra - lines changed 36, context: html, text, full: html, text

1bca724c3e143196d4d3ceea41fe15c0ac19fb70 Wed Apr 6 13:04:01 2022 -0700

• improved gateway page contents refs #29203
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 114, context: html, text, full: html, text

4a41483c4135ecdd79d04bd5dbfe7354d5a8c75e Wed Apr 6 13:05:07 2022 -0700

• prepear for trackDbOverrides operation in the future refs #29203
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 4, context: html, text, full: html, text

eb888fd5773e753ee783715599d662cc3d5e27fb Thu Apr 7 13:23:12 2022 -0700

• constructing the chainNet html page for a composite track refs #29203
  • src/hg/utils/automation/asmHubChainNetComposite.pl - lines changed 243, context: html, text, full: html, text

4f90338a4d065f90adf1de2d88ebf66be91efca8 Thu Apr 7 13:23:57 2022 -0700

• better cleanup no redmine
  • src/hg/utils/automation/doAugustus.pl - lines changed 1, context: html, text, full: html, text

a4f7d603028d5fdee198a7f2bb516bc6796862a8 Thu Apr 7 13:24:37 2022 -0700

• no need to have date time stamp on the description page refs #29203
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

45e061bdd61a8fdf439157af29822df1589f6c43 Thu Apr 7 13:25:31 2022 -0700

• add a hubDateName function and allow newdev to be used as a cluster refs #29203
  • src/hg/utils/automation/HgAutomate.pm - lines changed 54, context: html, text, full: html, text

895c7fceea79e43c9abf53a85b76ce7542cec328 Thu Apr 7 13:26:38 2022 -0700

• allow otherAligners directory in data downloads and gff3 gene file refs #29203
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 15, context: html, text, full: html, text

d6bd728e4dc7932d747fe49a8179f0141038823b Thu Apr 7 13:28:14 2022 -0700

• move function hubDateName() to HgAutomate.pm default track viz hide and correct html page reference refs #29203
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 50, context: html, text, full: html, text

2ac0b5334f5f839dfe9b853c804fe5d4b35c1175 Thu Apr 7 13:29:10 2022 -0700

• move the userTrackDb include to the end add correct chainNet.html for composite track and check for including trackDbOverrides refs #29203
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 15, context: html, text, full: html, text

658fb300956f1b2c395ffee56abfaf4bc8cfbafc Fri Apr 8 11:18:29 2022 -0700

• fixup ftp reference to be https for ftp.ncbi.nlm.nih.gov refs #29203
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 1, context: html, text, full: html, text

04393191d9ce3372ecf638c97f7ab84e3b7f2124 Fri Apr 8 16:04:20 2022 -0700

• running up Atlantic salmon per user request refs #29230
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

e3dc00ffa75d01a48dfb32178b9d77dab68ee7a5 Mon Apr 11 10:00:22 2022 -0700

• adding secondary fasta and 2bit delivery and correctly recognize an alternative defaultPosition refs #29203
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 4, context: html, text, full: html, text

a0a5a8da9739e17bbfe855a0cff62e3e8d88be52 Mon Apr 11 10:02:05 2022 -0700

• allow elimination of tracks via a dropTracks.lift file refs #29203
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 31, context: html, text, full: html, text