Commits for lrnassar

v422_preview to v422_preview2 (2021-10-04 to 2021-10-11) v422

3e628c524315ae7d3de8aac5d422c86cdabebcb7 Tue Oct 5 16:56:01 2021 -0700

• Releasing updated lrg tracks refs #24672
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 24, context: html, text, full: html, text

a64bc5a6cfe9756104a86f633b0f0a01772c4b83 Wed Oct 6 16:55:59 2021 -0700

• Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.
  • src/hg/utils/otto/clinGen/clinGenWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 77, context: html, text, full: html, text
  • src/hg/utils/otto/clinvar/clinvar.as - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/buildDecipher - lines changed 62, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/checkDecipher.sh - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/gwasWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/isca/iscaWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/lovd/lovd.long.as - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/lovd/lovd.short.as - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/omim/omimGene2ToBigBed.py - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/omim/omimUploadWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/omim/omimWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/otto.crontab - lines changed 4, context: html, text, full: html, text

29c0f7fde4830831982258fb7dece05f0cd39eae Fri Oct 8 09:34:40 2021 -0700

• Changing query command to curl as requests did not support ftp, and adding a sanitizing function to escape quotes when found in labels, refs #28008
  • src/utils/qa/hubPublicAutoUpdate - lines changed 20, context: html, text, full: html, text

cb4fbb9fa0dd10f12642472971a197b2b17a94a3 Mon Oct 11 08:36:03 2021 -0700

• Adding full path to hgsql util for cron environment.
  • src/utils/qa/hubPublicAutoUpdate - lines changed 2, context: html, text, full: html, text