Commits for hiram

v438_preview2 to v438_base (2022-10-03 to 2022-10-10) v438

61d34db4f91fbd325f16c3e9a5b87f66c6d4b462 Tue Oct 4 11:57:47 2022 -0700

• adding soybean legacy assembly GCF_000004515.4_Glycine_max_v2.0 per user request for a liftOver refs #30089
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text

6d9006164b9b861ba1d199c9c81b6ea40ababc1c Tue Oct 4 12:26:41 2022 -0700

• update instructions to include how to add locally developed tracks to the GenArk hub
  • src/hg/makeDb/doc/asmHubs/README.txt - lines changed 74, context: html, text, full: html, text

41e19d9efe6e606e34c4a832adc63c24ed27285b Tue Oct 4 14:26:32 2022 -0700

• beginning to add a share this link to be fixed up with the copy to clipboard functions no redmine
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 2, context: html, text, full: html, text

41d12b7ab39ffce5eba5fce2715a7afbe51667d2 Tue Oct 4 18:53:05 2022 -0700

• added an obsolete soybean assembly per user request no redmine
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 2, context: html, text, full: html, text

1e0a7a0350cbd56b4525ad015b783ed9e091e46d Wed Oct 5 10:01:37 2022 -0700

• adding copy link button to gateway page no redmine
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 2, context: html, text, full: html, text

2121928a798a7119f00eb7e198bd06cf4ea36d2f Wed Oct 5 10:14:36 2022 -0700

• correctly recognize the presence of the chain net files no redmine
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 4, context: html, text, full: html, text

4951a3f2ca22c980a415c231e59958197baec741 Wed Oct 5 10:41:05 2022 -0700

• correct Gene model labels on the ncbiGene (not really NCBI gene) track no redmine
  • src/hg/utils/automation/asmHubNcbiGene.pl - lines changed 27, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 17, context: html, text, full: html, text

2417266c7f2ef6fbaef4f292e8d160941225911e Wed Oct 5 10:47:32 2022 -0700

• clear up confusion of invertebrates with invertebrate only need one no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 169, context: html, text, full: html, text

83b8b215a8fb3c86ee95b43fba845bcba93e5ed3 Wed Oct 5 15:06:35 2022 -0700

• adding assembly 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/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text

33c36db157884a27c6557ec816985dfa55675757 Wed Oct 5 22:12:02 2022 -0700

• add onclick function to buttons of class copyLink no redmine
  • src/hg/js/hgGateway.js - lines changed 9, context: html, text, full: html, text

e9df5883fdd6fc3429b95c3f0df69ffd846766b6 Thu Oct 6 09:32:29 2022 -0700

• extra space and bold the link no redmine
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 1, context: html, text, full: html, text

5f37cb79891ed29155b740bf39f67f0a710ac362 Fri Oct 7 16:45:30 2022 -0700

• original description.html from GenArk instance before editing into zombie format

0412aa814e184e489d427bb34250355fee4a3cdd Fri Oct 7 16:53:37 2022 -0700

• I don't know what this is merging or why

010fc087ca305aee363153bb9d523aaad727d928 Fri Oct 7 16:58:27 2022 -0700

• monkeypox virus from NIAID Integrated Research Facility (IRF) https://www.flickr.com/photos/niaid/52103767506/ refs #29811
  • src/hg/htdocs/images/Monkeypox_virus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

fdbcbd6f5c97950df0bba8c319d026f3a61d338b Fri Oct 7 17:24:53 2022 -0700

• change hub text to zombie text refs #29811
  • src/hg/makeDb/trackDb/virus/mpxvRivers/html/description.html - lines changed 53, context: html, text, full: html, text

32fcbb4a69306091132bad1cedb83084e3c146fc Fri Oct 7 17:33:09 2022 -0700

• updated text refs #29811
  • src/hg/makeDb/trackDb/virus/mpxvRivers/html/assembly.html - lines changed 19, context: html, text, full: html, text

988fb9e9a5d07d53f4d70ff428f6e282a7587399 Fri Oct 7 17:50:28 2022 -0700

• cpgIslands recalculated refs #29811
  • src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra - lines changed 2, context: html, text, full: html, text

52f94f1f0d21752b3d8bcd3d879f2315bb2a6b96 Fri Oct 7 17:52:39 2022 -0700

• updated cpgIsland doc refs #29811
  • src/hg/makeDb/trackDb/virus/mpxvRivers/html/cpgIslands.html - lines changed 2, context: html, text, full: html, text

a530401a5ad42da837f0138689f123053e689191 Mon Oct 10 09:50:19 2022 -0700

• better indicate in the message that there will be a process to review the request no redmine
  • src/hg/htdocs/inc/garModal.html - lines changed 1, context: html, text, full: html, text