Commits for hiram

v414_preview2 to v414_base (2021-04-26 to 2021-05-03) v414

e55f16028cef4f090371dafece16faf736596822 Mon Apr 26 14:53:09 2021 -0700

• fixup correct ports for blat server refs #26658
  • src/hg/makeDb/doc/staAur2/initialBuild.txt - lines changed 2, context: html, text, full: html, text

2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700

• cleaning up crisprAll working data about 326 Tb no redmine
  • src/hg/makeDb/doc/calJac4/initialBuild.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam4/initialBuild.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam5/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/gorGor6/initialBuild.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/panPan3/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/regenCho1/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/regenRn1/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/rn7/initialBuild.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/wuhCor1/initialBuild.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/xenTro10/initialBuild.txt - lines changed 6, context: html, text, full: html, text

80a6b42f5687642d83715afc58c46a095610c2dc Tue Apr 27 08:10:49 2021 -0700

• liftOver chainNet to GCF_900094665.1 per user request and cleaning hive of crispr results refs #27344
  • src/hg/makeDb/doc/mm10.txt - lines changed 116, context: html, text, full: html, text

9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700

• hive cleaning running cleanup step for crispr tracks no redmine
  • src/hg/makeDb/doc/bosTau9/initialBuild.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/cotJap2/initialBuild.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/criGriChoV2/initialBuild.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/enhLutNer1/initialBuild.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text

0f52e6e2738f1a2a84e178d24e144efdeeb81a36 Tue Apr 27 14:14:21 2021 -0700

• running cleanup step on crispr tracks no redmine
  • src/hg/makeDb/doc/hg38/crispr.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/crisprAll.txt - lines changed 7, context: html, text, full: html, text

d4d57b07f6ef7aea3f07012a1f13abf642579d29 Tue Apr 27 14:15:38 2021 -0700

• correct name on lastz work directory refs #27321
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 2, context: html, text, full: html, text

28d715eb50876f2554505716fbd18b41e4c37b66 Tue Apr 27 14:17:49 2021 -0700

• now with a genesGtf download file refs #27388
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 2, context: html, text, full: html, text

eab50a6724ab3744ac395aeb57cecdcddb4a24ed Tue Apr 27 14:19:39 2021 -0700

• adding GCA_002844635.1_USMARCv1.0 Sus scrofa per user request refs #27388
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text

835f3ad66aac1927fa501bad9511e56f62d706c4 Tue Apr 27 14:36:26 2021 -0700

• lastz chainNet run per user request refs #27388
  • src/hg/makeDb/doc/susScr11/lastzRuns.txt - lines changed 102, context: html, text, full: html, text

44a2961414996cf4348b33a8c7daceacd3a3456e Tue Apr 27 14:50:55 2021 -0700

• completed lastz/chain/net to mm10 mm39 hg38 for rn7 release refs #26682
  • src/hg/makeDb/doc/mm39/lastzRuns.txt - lines changed 9, context: html, text, full: html, text

f13110a42ef4ef8ef9953b31c797022aa7a4f2ff Wed Apr 28 11:47:54 2021 -0700

• beginning lastz chainNet runs for 45-way no redmine
  • src/hg/makeDb/doc/rn7/lastzRuns.txt - lines changed 73, context: html, text, full: html, text

099d84d6dc2220c2401bc5ff18bc026d8651fd37 Thu Apr 29 22:54:47 2021 -0700

• turn on frames view refs #11636
  • src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra - lines changed 2, context: html, text, full: html, text

e941783cbc9cd3ec6af5f75b6969554fba9282e1 Thu Apr 29 23:05:28 2021 -0700

• adding frames procedure refs #11636
  • src/hg/makeDb/doc/hg38/cactus241way.txt - lines changed 65, context: html, text, full: html, text

6348b62549ccdad39b50fb4fd493d593b44ab31d Fri Apr 30 13:41:29 2021 -0700

• a supervisor script to the doBlastzChainNet script to run everything refs #26682
  • src/hg/utils/automation/pairLastz.sh - lines changed 434, context: html, text, full: html, text

67834b02649fc82ec728bd72a50309d87128007d Fri Apr 30 21:41:59 2021 -0700

• correct featureBits result file name refs #26682
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/pairLastz.sh - lines changed 19, context: html, text, full: html, text

c4e2ae3a2c37b244143589fbeda66de7e52f4ad7 Fri Apr 30 21:43:40 2021 -0700

• correct usage message refs #26682
  • src/hg/utils/automation/pairLastz.sh - lines changed 1, context: html, text, full: html, text