Commits for hiram

452c520b5692e08fa3977dc02d81d72d0116f69d Sun Aug 13 13:30:59 2023 -0700

adding GCA_018873775.2_hg01243.v3.0 human (HG01243 John Hopkins 2021) for user interested in a different chrY/CM034974.1 refs #31844
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

416dec4bcf1854bcc0cf18e6521379dd601a7231 Sun Aug 13 18:37:33 2023 -0700

allow -ram=Ng argument to get through to the para make command no redmine
- src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 12, context: html, text, full: html, text

5b4e0ab9dcf0345d588a88049923a619515ed211 Sun Aug 13 18:38:47 2023 -0700

allow -ram=Ng argument to get through to the para make command no redmine
- src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 1, context: html, text, full: html, text

167a944687bd484f0dc6c8821749c08053a2a0a5 Sun Aug 13 18:47:43 2023 -0700

add -ram argument to doAugustus to allow smaller ram size on the paraRun, this should be an argument to the paraRun setup no redmine
- src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text
- src/hg/utils/automation/doAugustus.pl - lines changed 9, context: html, text, full: html, text

7f114623aa512095de2a6a83cab942ca3829ea60 Tue Aug 15 10:18:17 2023 -0700

reChain the chains refs #31561
- src/hg/makeDb/doc/hg38/hprcReChain.txt - lines changed 108, context: html, text, full: html, text

de24277b1786c47fa9ba420c0858f56bb648f981 Tue Aug 15 11:50:57 2023 -0700

add the re-chain HPRC alignments refs #31561
- src/hg/makeDb/trackDb/human/hg38/chainsReHprc.ra - lines changed 824, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

2ce0876f4171ec948fb7705a9f42047e0f059eea Wed Aug 16 09:24:11 2023 -0700

get the ebiGene and ensGene tests correct and protect against missing liftOver file in a blat directory refs #31844
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 9, context: html, text, full: html, text

ee2d91d9f91e87f02680184075bf8592b3a6ec93 Wed Aug 16 10:06:22 2023 -0700

adding a number of primates discovered in a paper from the Illumina primate project refs #31528
- src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 36, context: html, text, full: html, text

e77b7fbee5c6e7693e1ebb796a0af57cccd6fcfe Thu Aug 17 11:49:42 2023 -0700

add the re-net HPRC alignments refs #31561
- src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra - lines changed 731, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

8f584e5787939093cc317e78db7f5ceb2927bc1f Thu Aug 17 19:04:22 2023 -0700

longer labels on the subpopulations refs #31561
- src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra - lines changed 1, context: html, text, full: html, text

baf353f458d71234e27d15f6c1a3ef8cf703625a Thu Aug 17 19:24:18 2023 -0700

now ordered by population then subpopulation and with longer subpopulation labels refs #31561
- src/hg/makeDb/trackDb/human/hg38/chainsReHprc.ra - lines changed 596, context: html, text, full: html, text

bc3bb05dc921ff5bfca856abaf519bb2eab9134e Thu Aug 17 19:27:19 2023 -0700

with correct priorities refs #31561
- src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra - lines changed 89, context: html, text, full: html, text

6d71edab2f5be83d635411c1cd3de8e343c26115 Sun Aug 20 15:10:13 2023 -0700

now with phyloP track refs #31528
- src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra - lines changed 57, context: html, text, full: html, text