Commits for hiram

v404_preview to v404_preview2 (2020-08-31 to 2020-09-07) v404

d4801b8da713162acb83051810b05d175803d84f Mon Aug 31 10:26:14 2020 -0700

• updated with Ensembl v101 additions and a couple new UCSC database genomes refs #26145
  • src/hg/makeDb/doc/assemblyEquivalence/update.2020-08-31.txt - lines changed 173, context: html, text, full: html, text

00f883e4f3d8479516b649b22905037eb9dd0168 Mon Aug 31 13:20:36 2020 -0700

• definitions for v101 update refs #26145
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1550, context: html, text, full: html, text

71afd9d91414afe788f7b4fc294dc9973b4baad3 Mon Aug 31 14:57:08 2020 -0700

• construct symLinks into goldenPath for GTF file and archive files refs #26415
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 36, context: html, text, full: html, text

32029e8336069dd159be8945e30c6d9e9d9f3c98 Mon Aug 31 15:09:33 2020 -0700

• construct symLinks into goldenPath for GTF file and archive files refs #26415
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 4, context: html, text, full: html, text

dc0ff6b7cda41fce2d04b9cce778901be0c760bf Tue Sep 1 10:57:30 2020 -0700

• add duplicate verification refs #26145
  • src/hg/makeDb/doc/assemblyEquivalence/update.2020-08-31.txt - lines changed 9, context: html, text, full: html, text

645b05900827c9a0c59641d6a0a4be33846dc5a3 Tue Sep 1 12:48:38 2020 -0700

• better descriptive name in column 2 of the GTF file refs #26415
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 9, context: html, text, full: html, text

7ad632c236376136c01336310533ebec0a041bd9 Tue Sep 1 13:46:51 2020 -0700

• version 101 procedure added refs #26145
  • src/hg/makeDb/doc/makeEnsembl.txt - lines changed 207, context: html, text, full: html, text

51e48525d609b69f4168bcc624e9f86fa9e05d39 Wed Sep 2 10:01:54 2020 -0700

• added calJac4 to the build refs #24074
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac4/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac4/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac4/gold.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra - lines changed 8, context: html, text, full: html, text

070e34d6b3cad774a80daaa4277a9666b68917b9 Wed Sep 2 10:16:13 2020 -0700

• mm39 chainNet done refs #22271
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 18, context: html, text, full: html, text

abd5b59c9c6ad66a6b1a8c30814099f39582923b Wed Sep 2 10:59:45 2020 -0700

• show blatServer entries found refs #19883
  • src/hg/utils/automation/verifyBrowser.pl - lines changed 2, context: html, text, full: html, text

360bab4f0495de7c98aa842d94aa6a6cde876324 Wed Sep 2 17:32:14 2020 -0700

• running up window masker refs #24074
  • src/hg/makeDb/doc/calJac4/initialBuild.txt - lines changed 1382, context: html, text, full: html, text

b3623d772cd2a857c4cd7aa5ac82b0a9e1c63354 Thu Sep 3 11:45:12 2020 -0700

• adding search rule for gold/assembly track refs #24074
  • src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra - lines changed 5, context: html, text, full: html, text

bbd6bb52c2407aa5c46725fef114aed1a6b5b396 Thu Sep 3 12:49:32 2020 -0700

• Added calJac4 mouse; refs #24074
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text

436c9c0d4b1b38ad5cd6ad29e0065f36b7440c87 Thu Sep 3 12:50:53 2020 -0700

• Added calJac4 - marmoset refs #24074
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 2, context: html, text, full: html, text

be590b26ca854e89606338fcfecb9c9ac85273b8 Thu Sep 3 12:53:49 2020 -0700

• ready for genbank run refs #24074
  • src/hg/makeDb/doc/calJac4/initialBuild.txt - lines changed 261, context: html, text, full: html, text

92f411c1e49f135fe0908dec77fbbc3e82a50157 Thu Sep 3 15:28:59 2020 -0700

• starting chainNet calJac4 to mm10 and hg38
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 69, context: html, text, full: html, text

00e3608ca2baa3d21e228a1611ca8c580bc9e65d Fri Sep 4 23:27:53 2020 -0700

• calJac4 lastz chainNet done to mm10 and hg38 refs #24074
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 13, context: html, text, full: html, text