Commits for hiram

v473_preview2 to v473_base (2024-10-21 to 2024-10-28) v473

2df91f181b1639297e87adfaee146fedcebd2f4a Mon Oct 21 13:53:37 2024 -0700

• now using hgwdev cluster for lastz runs and lastz only needs 3gb memory to run refs #34688
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/pairLastz.sh - lines changed 6, context: html, text, full: html, text

ba227c00ba4786dcbe2482cc6282e36e867c778b Tue Oct 22 15:06:25 2024 -0700

• something fishy here not sure what refs #34685
  • src/hg/utils/automation/HgAutomate.pm - lines changed 3, context: html, text, full: html, text

7e831339b05c777662c2f25fbddac1ad3543f2e1 Tue Oct 22 22:28:38 2024 -0700

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

e971cb3711d443360ac4a480b8dca4322b559cfa Wed Oct 23 16:54:01 2024 -0700

• no longer send out hub.txt files, obsolete refs #34689
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 8, context: html, text, full: html, text

3d843800810c738ed63e1af3f471c4c3f6316264 Wed Oct 23 17:10:21 2024 -0700

• no longer send out genomes.txt files, obsolete refs #34689
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 3, context: html, text, full: html, text

358e762de07c37fdfe7b8a0a03f16341e4fddf11 Wed Oct 23 17:21:16 2024 -0700

• adding assemblies for BRC project refs #34337
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 44, context: html, text, full: html, text

d72fcfd04dee8c6a6362a7dce10157f06b1af6f4 Wed Oct 23 17:49:13 2024 -0700

• no longer making the genomes.txt or hub.txt files, obsolete refs #34689
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 14, context: html, text, full: html, text

098291ec429c92f2fae1b383c272bc5558ce6dfd Thu Oct 24 14:38:18 2024 -0700

• mistake, the hub.txt files do go out for the individual assembly refs #34689
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 8, context: html, text, full: html, text

fb4ea088b4e255ba27b04ae59e86644dabe6eda7 Thu Oct 24 23:13:25 2024 -0700

• adding NCBI link outs on NCBI RefSeq gene tracks refs #34704
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 3, context: html, text, full: html, text

4f1877c2974ee37a984000e1add2c4c27da0de7b Fri Oct 25 18:48:17 2024 -0700

• the TMPDIR needs to be set locally on the para node not where the driver script is making the sub-script refs #34685
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/doWindowMasker.pl - lines changed 32, context: html, text, full: html, text

0cf3bcb238f681f3df0decac63b08b4953d3f455 Sat Oct 26 23:25:21 2024 -0700

• getting TMPDIR set correctly refs #34685
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 20, context: html, text, full: html, text