Commits for hiram

v466_preview to v466_preview2 (2024-05-20 to 2024-05-27) v466

6b4b6d8db2ca21b06d57b1507c0e67f01338bf33 Mon May 20 12:39:06 2024 -0700

• update underway this the first 18 done refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 18, context: html, text, full: html, text

8fd2016b6c0e6a6c0bccbf47f2133124c5e6657e Mon May 20 12:48:30 2024 -0700

• this will make symLinks happen twice but it is needed and now making a chain net listing while running refs #29545
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 2, context: html, text, full: html, text

1e8c52aca6900f6f3ce8b31e79cd6b625715ca39 Mon May 20 13:11:37 2024 -0700

• four updates genbank to refseq refs #29545
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 8, context: html, text, full: html, text

13488a498e6b5238accdbf32c140ed30e30d173c Mon May 20 14:48:43 2024 -0700

• correctly get mkSymLinks to run before mkGenomes refs #29545
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 11, context: html, text, full: html, text

ed7414028de9887b9fe8d562758a0af09dedcd8f Thu May 23 18:31:52 2024 -0700

• better default visibilities no redmine
  • src/hg/utils/automation/asmHubChainNetTrackDb.pl - lines changed 26, context: html, text, full: html, text

1391f50a576e35bd691d3e3898475b5637b88976 Thu May 23 18:32:31 2024 -0700

• correct naming of files when porting GCF refSeq to equivalent GCA assembly no redmine
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 18, context: html, text, full: html, text

9374faeb653ab0653e07e6ba890d6531395ae476 Fri May 24 09:59:56 2024 -0700

• correctly identify the source for the genes when coming from GCF onto GCA no redmine
  • src/hg/utils/automation/asmHubNcbiRefSeq.pl - lines changed 16, context: html, text, full: html, text

e76c704d9c5c6dfa06f7d7e15387fd14f651d9bf Fri May 24 10:09:39 2024 -0700

• correct FTP path no redmine
  • src/hg/utils/automation/asmHubNcbiRefSeq.pl - lines changed 3, context: html, text, full: html, text

27a61987f2692b2fad37a9faada47b927f568e1e Fri May 24 10:11:44 2024 -0700

• correct ftp to https for references to ftp.ncbi.nih.gov no redmine
  • src/hg/utils/automation/asmHubHtml.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubNcbiGene.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubWindowMasker.pl - lines changed 1, context: html, text, full: html, text

08300d3c6b6f4211a16bf497c40ae6722242d4d4 Fri May 24 14:05:36 2024 -0700

• script to add RefSeq genes to a GenBank assembly no redmine
  • src/hg/utils/automation/refSeqOnGenBank.py - lines changed 194, context: html, text, full: html, text

d258476e0cc734212538e8ab0a7509acb8b24aaa Fri May 24 14:10:17 2024 -0700

• remove cruft no redmine
  • src/hg/utils/automation/refSeqOnGenBank.py - lines changed 13, context: html, text, full: html, text

8c99a44e8855b4d78a741f91c02abc603c7ca7ca Fri May 24 14:29:24 2024 -0700

• the version check stuff does not actually work
  • src/hg/utils/automation/refSeqOnGenBank.py - lines changed 13, context: html, text, full: html, text

f22a96abc0a0fe44ef9a12d57571609f13473435 Fri May 24 15:54:27 2024 -0700

• adding assembly GCA_002743455.1_CAU_duck1.0 common mallard (Pekin duck 2017) per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text

13d6c761cb546b415419da0671931101f5f9a5be Sun May 26 16:57:57 2024 -0700

• RefSeq update finished primates refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 6, context: html, text, full: html, text

f81d9d27f273824d88236ee48736f674fe441092 Mon May 27 08:52:41 2024 -0700

• sciName for mosquitoes, bees, moths and sponges no redmine
  • src/hg/makeDb/doc/asmHubs/commonNames.pl - lines changed 5, context: html, text, full: html, text

a1e069cada2a0a440988bc879b09a8c146e284a2 Mon May 27 09:32:24 2024 -0700

• catch up run.list with tsv entries no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 8, context: html, text, full: html, text

5a43b9ffe0eae7367e4b59e9ae9422d7718621bd Mon May 27 09:33:30 2024 -0700

• refseq update adding 8 refs #29545
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 21, context: html, text, full: html, text