Commits for hiram

v413_preview2 to v413_base (2021-04-05 to 2021-04-12) v413

0cf6d0bf916e95eede2ab70d04efc35de51573a2 Mon Apr 5 11:41:57 2021 -0700

• track has removed its priority line no redmine;
  • src/hg/hubApi/tests/expected/schema10.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

24662cf7d67a02bc0a1dab62b3be93cdc97eb800 Mon Apr 5 12:42:49 2021 -0700

• improving errro messages in case of dynamic server overload refs #26658
  • src/hg/hgBlat/hgBlat.c - lines changed 19, context: html, text, full: html, text

4e762a020077ea49d08f2c60b4d56a0d59e1bd29 Mon Apr 5 14:37:55 2021 -0700

• better error message in gfClient when dynamic blat server failure refs #26658
  • src/gfClient/gfClient.c - lines changed 32, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 2, context: html, text, full: html, text
  • src/inc/errCatch.h - lines changed 10, context: html, text, full: html, text

31cfa0823734a570e9aabdbfd730dbd01f0b0a85 Tue Apr 6 13:51:13 2021 -0700

• eliminate the trailing ^M on the taxId and testing blat-backup refs #26658
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 3, context: html, text, full: html, text

105dbccea1c736dbd8393e3e3d55d85a2f8f922d Tue Apr 6 13:52:53 2021 -0700

• now with host argument on verify to verify with different servers refs #26658
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 15, context: html, text, full: html, text

8b9550f224b17e9118820b82f88655a589d9e383 Tue Apr 6 13:55:04 2021 -0700

• eliminate single gapOverlap track and getting ready for lastz chainNet tracks refs #26658
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 23, context: html, text, full: html, text

bef062c8d38d8813621688d6cb115d9f9f9e0b3d Tue Apr 6 13:58:19 2021 -0700

• correctly send gtf file to bigZips/genes refs #26428
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 1, context: html, text, full: html, text

d17d8aa5904721432031873676eb9fdef45a1c25 Wed Apr 7 09:44:38 2021 -0700

• adding sheep vs. hg38 refs #27231
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 66, context: html, text, full: html, text

68d6d9b391f13a9f09724ee7943e60ebf1df108b Wed Apr 7 10:07:26 2021 -0700

• add definitions for sheep/GCF_002742125.1 rn7 and xenTro10 refs #27321
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 19, context: html, text, full: html, text

d5849c76b7b13e3189e1ce67035ba9695a821122 Wed Apr 7 16:02:04 2021 -0700

• lastz chainNet to assembly hub GCF_002742125.1 refs #27321
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 103, context: html, text, full: html, text

697433c3bb2bfd1ea3a61f9715ed2bff32210071 Thu Apr 8 10:00:06 2021 -0700

• adding vaccine track refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra - lines changed 18, context: html, text, full: html, text

9e8bdeb3e12205577bff31b067a4b54aec7059f5 Thu Apr 8 12:27:18 2021 -0700

• initial discussion refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 78, context: html, text, full: html, text

b18ba7e510b3924376e1119d8bec7f308fbaf680 Thu Apr 8 15:05:05 2021 -0700

• filling in the description page refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 34, context: html, text, full: html, text

c99c3332ebb86e79017f2a9687a637b6c6f9da68 Thu Apr 8 15:06:54 2021 -0700

• filling in the description page refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text

8802f297ea83400417f0554c50c41cf922ba14df Fri Apr 9 10:42:03 2021 -0700

• completed track description page refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra - lines changed 2, context: html, text, full: html, text

4b34f0f7f41bc83f4944cd82416656354cb8438a Fri Apr 9 10:53:30 2021 -0700

• correct track name refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra - lines changed 1, context: html, text, full: html, text

61caa523f9d5b4fa0a65f08ef60dcb4d4a9d2e3d Fri Apr 9 10:55:11 2021 -0700

• correct track group refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra - lines changed 1, context: html, text, full: html, text

c8d4a396979b1bcf0ec166d9ce5ce9e707f68d8d Fri Apr 9 11:06:24 2021 -0700

• procedure for vaccine track refs #27312
  • src/hg/makeDb/doc/wuhCor1/vaccines.txt - lines changed 204, context: html, text, full: html, text

4588a5528433ea59ad7a9a5c53df3db57dc9426d Fri Apr 9 12:23:35 2021 -0700

• adding references refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 7, context: html, text, full: html, text

964019044e25ffa2e215e658f470d647a487bfa6 Fri Apr 9 16:46:39 2021 -0700

• correct discussion of the two AA differences refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 13, context: html, text, full: html, text

c975a54c98d0d9df901018c20622bbf14cc4e029 Fri Apr 9 16:51:24 2021 -0700

• color the PP AAs in the sequence refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text

a9bb1f10c8525ec26075305820047acba867d8fb Fri Apr 9 17:03:26 2021 -0700

• correct variation notation refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text

680a791e910f94be537ad381e06bbb68afd9f4ca Fri Apr 9 20:14:52 2021 -0700

• bold text on the PP AAs refs #27312
  • src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.html - lines changed 1, context: html, text, full: html, text