Commits for hiram

v497_base to v498_preview (2026-04-20 to 2026-04-27) v498

633cc56e1b1043b0ab6e1fd0e9b90154e2c03c0c Mon Apr 20 13:00:51 2026 -0700

• document procedure for import of VGP 577-way maf result refs #34370
  • src/hg/makeDb/doc/vgp577way/linkSizes.sh - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/mafCoverage.pl - lines changed 185, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/mkIRowsJL.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/mkNbeds.sh - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/queryCounts.sh - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/sumBlocks.py - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgp577way/vgp577way.txt - lines changed 366, context: html, text, full: html, text

597461b5be887ae783de796a596034cc2d946448 Mon Apr 20 16:09:41 2026 -0700

• adding assemblies per user requests
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

1a9024a64f170308fb0d1adcb548399f960e46c2 Mon Apr 20 23:51:10 2026 -0700

• NCBI changed the name of GCA_030272585.1
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text

435e92d0ad49164d1b5b156e3fb5ef5ff7b19041 Tue Apr 21 12:29:50 2026 -0700

• make the ottoRequest table a bit more generic so it can handle both liftOver and assembly requests refs #31811
  • src/hg/inc/ottoRequest.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.as - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.c - lines changed 51, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.sql - lines changed 5, context: html, text, full: html, text

908c2b249f2cea98192862b2ce49af1a43e48838 Tue Apr 21 12:37:24 2026 -0700

• updated ottoRequest table schema for more general requests refs #31811
  • src/hg/hubApi/liftOver.c - lines changed 1, context: html, text, full: html, text

3e3270b639bae3a1dee7a4a69ffda4a6298c81cf Tue Apr 21 12:44:10 2026 -0700

• adding liftRequest.js refs #31811
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text

7d049679cd9efc4dacc25fc0f181e85d7221d48b Tue Apr 21 12:44:36 2026 -0700

• adding liftRequest.js refs #31811
  • src/hg/htdocs/style/makefile - lines changed 1, context: html, text, full: html, text

113937fa86799fcf930f93aade0355a698088982 Tue Apr 21 12:45:53 2026 -0700

• fixups to avoid jshint errors refs #31811
  • src/hg/js/liftRequest.js - lines changed 26, context: html, text, full: html, text

fcfb91470c294d3b991dbd0d24cba67de9ed65cb Tue Apr 21 14:20:57 2026 -0700

• create ottoRequest cron watch script refs #31811
  • src/hg/inc/ottoRequest.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 149, context: html, text, full: html, text

1915cefe1c6dd5746ee2c3e8a9ba9cfd4ad4e3b5 Tue Apr 21 14:45:24 2026 -0700

• turning on ottoRequest watch script refs #31811
  • src/hg/utils/otto/otto.crontab - lines changed 4, context: html, text, full: html, text

f841658912e8c8441e745b2bfdbb86b7c270d811 Tue Apr 21 14:52:59 2026 -0700

• run ottoRequest.py every minute refs #31811
  • src/hg/utils/otto/otto.crontab - lines changed 2, context: html, text, full: html, text

e8b16ae601a09359f4b4fa543d365f3d02bd6e6d Wed Apr 22 13:25:09 2026 -0700

• listing of assemblies with names and clade groupings for this 577-way alignment refs #34370
  • src/hg/makeDb/doc/vgp577way/577.acc.sciName.comName.clade.tsv - lines changed 577, context: html, text, full: html, text

a83601f74d58302315fa0e3c151ff29df6637afb Wed Apr 22 14:39:15 2026 -0700

• more general procedure refs #34370
  • src/hg/makeDb/doc/vgp577way/vgp577way.txt - lines changed 185, context: html, text, full: html, text

46668bb54c3c8a7a57bda515be6881edb2382563 Wed Apr 22 14:55:23 2026 -0700

• correctly connecting scoringMatrix input to kegAlign scores refs #31811
  • src/hg/utils/automation/kegAlign.json.ga - lines changed 170, context: html, text, full: html, text

584b69eff038b10c2176d2b9299c356af21288cc Wed Apr 22 16:30:53 2026 -0700

• initial scripts to run the galaxy workflow based off of the ottoRequest table entries refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 29, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/dbDb.name.clade.tsv - lines changed 239, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 146, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 258, context: html, text, full: html, text

83f8234095a0b5e6edb8aaaeabb8e78443830ea3 Thu Apr 23 13:48:43 2026 -0700

• turn off the email notification from here, let the otto cron job do the email refs #31811
  • src/hg/hubApi/liftOver.c - lines changed 6, context: html, text, full: html, text

b3a76833aa84a341e86d0bacef2ff1f6b9b44851 Thu Apr 23 14:30:24 2026 -0700

• rename workflowId column to buildDir and expand its size refs #31811
  • src/hg/hubApi/liftOver.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/ottoRequest.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.sql - lines changed 2, context: html, text, full: html, text

398e258ed1330421291f943298e7f801f7b05bf8 Thu Apr 23 15:05:02 2026 -0700

• and send notification email to the requesting user refs #31811
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 41, context: html, text, full: html, text

6d8144be131a358037daea03610b22315527f26f Thu Apr 23 15:12:32 2026 -0700

• better recognition of errors in the workflow refs #31811
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 36, context: html, text, full: html, text

f0b8830616972bad195079b7ce775c919ff1e25f Thu Apr 23 15:13:50 2026 -0700

• correctly decide which is going to be target and query based on the N50 sizes of the two given assemblies refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 99, context: html, text, full: html, text

3bb21ba2c8ac7f60effdb9c311ff27e4016f8e57 Thu Apr 23 15:14:35 2026 -0700

• script to use in hiram cron tab to watch for new requests and get the galaxy workflow running refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 66, context: html, text, full: html, text

d8ade6071b7e59f93d5b703b3c024b345871dce1 Fri Apr 24 08:55:58 2026 -0700

• becoming complete process refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 68, context: html, text, full: html, text

1cbaa9ddcb7a13929a2217db78d6b36ff738fe15 Fri Apr 24 10:52:34 2026 -0700

• doneStatus can simply be status refs #31811
  • src/hg/hubApi/liftOver.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/ottoRequest.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/ottoRequest.sql - lines changed 2, context: html, text, full: html, text

f5cece60b38bd8c2cfd57acf2abb972d66edb6d9 Fri Apr 24 11:43:36 2026 -0700

• rename doneStatus to just status and correctly set status codes refs #31811
  • src/hg/utils/otto/userRequests/README.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequest.py - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestAlign.sh - lines changed 138, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 27, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/workflowMonitor.sh - lines changed 24, context: html, text, full: html, text