Commits for hiram

v442_preview to v442_preview2 (2022-12-19 to 2023-01-03) v442

9df5ecf8842547ecb2a7c6fd2338a3f3a6fb5e26 Tue Dec 20 10:39:21 2022 -0800

• setup the custom RepeatModeler lib for download reference no redmine
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 5, context: html, text, full: html, text

24d667a6353af7e3d009ff35beb21f85dc40984d Tue Dec 20 10:40:08 2022 -0800

• correctly make symLinks for chainNet files at the time they actually exist no redmine
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 12, context: html, text, full: html, text

d08be258b2272b1ca51a89759cb88027fd6df84d Tue Dec 20 10:57:03 2022 -0800

• fixup gbdb locations for chain nets to GCF_009829145.1 no redmine
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.rbestNet.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.syntenicNet.ra - lines changed 4, context: html, text, full: html, text

5c6eeb845281a9cf407dcadd3480b1c65bfb48c7 Wed Dec 21 11:00:05 2022 -0800

• mistaken left on forced UCSC names for alt sequences no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

c0934691ab46714dedde3271b09d15f55d4a4471 Thu Dec 22 22:43:59 2022 -0800

• this is progress with an important note about cleaning up left over garbage
  • src/hg/makeDb/doc/assemblyEquivalence/update.2022-11-14.txt - lines changed 460, context: html, text, full: html, text

249f1c6c7231ede3da49dd949eaffb491e5d48cf Fri Dec 23 08:39:41 2022 -0800

• correct processing of alternatie and patch sequences no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 20, context: html, text, full: html, text

4dc9aaa85b70bdd4fd58d77b323147e28dbe16e6 Sat Dec 24 13:01:30 2022 -0800

• fixup new rmToTrackHub.pl usage no redmine
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 12, context: html, text, full: html, text

d7d65ade9824fda1d981e1f9692860e243dd76a1 Mon Dec 26 21:01:46 2022 -0800

• "do not have the same name bash script as doRepeatMasker.pl no redmine
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 1, context: html, text, full: html, text

b032eee9e1cec0a1cb46ccff207a7a99b0a94e00 Wed Dec 28 22:17:38 2022 -0800

• run repeatModeler in /dev/shm for better performance no redmine
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 23, context: html, text, full: html, text

4f202ee8fcfdcec142628ab0da1ba73fe81b72fb Sat Dec 31 10:52:42 2022 -0800

• correctly use the tmpDir for parasol no redmine
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 19, context: html, text, full: html, text

f0f02218613a6cce438e7ce73694f7539587118d Mon Jan 2 09:33:12 2023 -0800

• preserve the do.log during the rsync no redmine
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 2, context: html, text, full: html, text