Commits for hiram

v490_preview2 to v490_base (2025-10-27 to 2025-11-03) v490

1be49dce000ce111f3d1a81b4aef086e6d579f4c Mon Oct 27 16:43:09 2025 -0700

• reset the scripts to only push from hgwdev to hgwbeta refs #35575
  • src/hg/utils/otto/genArk/pushNewOnes.sh - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/quickLiftNew.sh - lines changed 46, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/whatIsNew.sh - lines changed 45, context: html, text, full: html, text

773fabd8bcd1acc5bdcc5dc27ef7fba3c8050c76 Tue Oct 28 11:13:34 2025 -0700

• script to use by cluster admin to push out from hgwbeta to the RR refs #35575
  • src/hg/utils/otto/genArk/pushFromBetaToRR.sh - lines changed 47, context: html, text, full: html, text

207b18d3428f769b443fb13c35fdfc3af2444936 Wed Oct 29 09:56:14 2025 -0700

• raise CPU limit to 12 for the chain step refs #36546
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

e24709a4ec08445450979b1ba907671aafacc13c Wed Oct 29 09:56:14 2025 -0700

• raise memory limit to 12G for the chain step refs #36546
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

b9326c31b78f235181798c5df993f610db395049 Wed Oct 29 10:59:37 2025 -0700

• raise memory limit to 12G for the chain step refs #36546
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 1, context: html, text, full: html, text

163e38242d3cd8d004882cfef7a557c9944f59e3 Wed Oct 29 11:24:47 2025 -0700

• default cluster should be hgwdev not obsolete ku refs #36546
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

f7b43908c094bc252185289d72755b4f55b0f623 Wed Oct 29 16:45:30 2025 -0700

• beginning of an auto script to run the longdust procedure on an assembly
  • src/hg/utils/automation/doLongdust.pl - lines changed 275, context: html, text, full: html, text

6e7e7ed56bc4de54088e81e32068fb14c4dfaac3 Thu Oct 30 11:44:32 2025 -0700

• may be complete at this time
  • src/hg/utils/automation/doLongdust.pl - lines changed 16, context: html, text, full: html, text

a02fe4b3289da1d30d52ba60b769644e9a3d8454 Thu Oct 30 12:51:55 2025 -0700

• correct start up for the bedResult step
  • src/hg/utils/automation/doLongdust.pl - lines changed 4, context: html, text, full: html, text

afb5dbee2256da1db93064340dcf4508aee3955f Fri Oct 31 14:26:41 2025 -0700

• needs to have a db argument and write out a version.txt file
  • src/hg/utils/automation/doLongdust.pl - lines changed 11, context: html, text, full: html, text

b6999503af29255b9956d018763bdc6b46965d36 Fri Oct 31 14:42:29 2025 -0700

• more cleanup
  • src/hg/utils/automation/doLongdust.pl - lines changed 1, context: html, text, full: html, text

64f5aaf6b778b991cadb76a605325760cef3fd71 Fri Oct 31 15:25:00 2025 -0700

• Adding Gene Meyers' FasTAN tandem repeat finder procedure
  • src/hg/utils/automation/doFasTAN.pl - lines changed 300, context: html, text, full: html, text

582e3e62507cc29716f2d19896a4ba90d927ce53 Fri Oct 31 15:32:13 2025 -0700

• Correct Myers name spelling
  • src/hg/utils/automation/doFasTAN.pl - lines changed 1, context: html, text, full: html, text

0987ef2a57422e1b7a0227b9abd7fadac942e2e8 Fri Oct 31 15:36:18 2025 -0700

• bed file definition of the output from FasTAN
  • src/hg/lib/fasTAN.as - lines changed 9, context: html, text, full: html, text

8c9fa3d2aef3a6cd7681748602fc303842196f5e Fri Oct 31 15:46:47 2025 -0700

• correct possessive
  • src/hg/lib/fasTAN.as - lines changed 1, context: html, text, full: html, text

39c14307224404251ce37952391cc6b7babea0f7 Fri Oct 31 15:47:31 2025 -0700

• with specific fasTAN.as schema definition
  • src/hg/utils/automation/doFasTAN.pl - lines changed 6, context: html, text, full: html, text