Commits for hiram

v422_base to v423_preview (2021-10-18 to 2021-10-25) v423

90af857c47a2063649df6d9526c94de4989f12ec Tue Oct 19 12:03:52 2021 -0700

• mouse and date palm lastz runs completed per user requests refs #28365 #28302
  • src/hg/makeDb/doc/asmHubs/lastzRuns.txt - lines changed 243, context: html, text, full: html, text

f3236a4aa3d7e74b63c7d2cb2f9e3b37ac7858b8 Tue Oct 19 12:22:57 2021 -0700

• beware the name date vs. date palm refs #28365
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 5, context: html, text, full: html, text

a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700

• scripts to run the NCBI RefSeq update automatically refs #24735
  • src/hg/utils/otto/ncbiRefSeq/archiveOne.sh - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/ottoNcbiRefSeq.sh - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/prevHg19.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/prevHg38.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/prevMm10.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/prevMm39.sum - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runHg19.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runHg38.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runMm10.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runMm39.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh - lines changed 63, context: html, text, full: html, text

d5dd5a3cb96a68a3bc78d07e8247fc03036e2a73 Tue Oct 19 14:01:21 2021 -0700

• scripts to run the NCBI RefSeq update automatically refs #24735
  • src/hg/utils/otto/ncbiRefSeq/README.txt - lines changed 5, context: html, text, full: html, text

8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700

• scripts for the GRC Incident otto job no redmine
  • src/hg/utils/otto/grcIncident/README.txt - lines changed 57, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/grcUpdate.sh - lines changed 120, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/parseGff.pl - lines changed 44, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/runUpdate.sh - lines changed 112, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/verifyTransfer.sh - lines changed 47, context: html, text, full: html, text

7ca589e9eb061fa0b78b02f616c6b28c85fc15e5 Thu Oct 21 11:18:31 2021 -0700

• indicate the cron tab entry
  • src/hg/utils/otto/grcIncident/README.txt - lines changed 6, context: html, text, full: html, text

ed292c11c5008eec8dd80894e385fead2d77a97c Thu Oct 21 11:59:45 2021 -0700

• correct result when the first contig satisifies the measurement no redmine
  • src/hg/utils/automation/n50.pl - lines changed 4, context: html, text, full: html, text

9d4bef0d3eb7ba60d763868e2db43256281e38ab Fri Oct 22 13:31:37 2021 -0700

• lastz runs to golden hamster refs #28333
  • src/hg/makeDb/doc/asmHubs/lastzRuns.txt - lines changed 505, context: html, text, full: html, text

e7c438c709822b66b2cad226d2a58940823e7b00 Fri Oct 22 14:06:41 2021 -0700

• adding chainNet for golden hamster GCF_000349665.1 refs #28333
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 95, context: html, text, full: html, text

0fd53fc90dcc6fd4deca96abee94ea5344a73f39 Sat Oct 23 15:25:09 2021 -0700

• adding Paramecium_tetraurelia_strain_d4-2 no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 54, context: html, text, full: html, text

10495af5529be614efb01145d78ce0509c2c9b67 Sat Oct 23 15:28:37 2021 -0700

• adding Paramecium tetraurelia (d4-2 2017) no redmine
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text