Commits for lrnassar

v445_preview2 to v445_base (2023-03-06 to 2023-03-13) v445

19248340c20f05707fb11f937edff1703c4ae98c Tue Mar 7 16:48:14 2023 -0800

• Adding the evaSnp4 description page, refs #30320
  • src/hg/makeDb/trackDb/evaSnp4.html - lines changed 213, context: html, text, full: html, text

fba0bd9bb1eb54ead37e38b5d6ac9cc040c77ffd Tue Mar 7 16:51:30 2023 -0800

• Adding pennantIcon for new track, refs #30320
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 26, context: html, text, full: html, text

f41fc338ea8d2f30b241f4af099527bcac02b1c8 Wed Mar 8 16:54:00 2023 -0800

• Ongoing work to standardize otto, removing individual ottomeister in favor of a central email repo people can subscribe to, refs #28331
  • src/hg/utils/otto/clinGen/clinGenWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/dbVar/dbVarWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/decipherWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/updateHgcentral.sh - lines changed 1, 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/grcIncident/grcUpdate.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/grcIncident/runUpdate.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/lrg/lrgWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh - lines changed 2, 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/orphanet/orphanetWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/otto.crontab - lines changed 14, context: html, text, full: html, text

d93d32ad4b79aff0c9ac7d10f62609183287cd66 Wed Mar 8 17:01:16 2023 -0800

• Removing a heartbeat message. It has been running this way on hive for a while and it all seems well. No RM.
  • src/hg/utils/otto/decipher/checkDecipher.sh - lines changed 3, context: html, text, full: html, text

1cb645d2d695768372404159511419112e4000f6 Wed Mar 8 17:11:32 2023 -0800

• Disabling heartbeat messages to reduce spam. These have been running this way for a while with no noticible issues. Refs #28331
  • src/hg/utils/otto/decipher/decipherWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/omim/checkOmimUpload.sh - lines changed 2, context: html, text, full: html, text

4745c92b18f0c01f24e255944c02140a8b231a22 Thu Mar 9 10:44:40 2023 -0800

• Commenting out CGAP lines since the database is defunct now, refs #30695
  • src/hg/hgGene/hgGeneData/links.ra - lines changed 5, context: html, text, full: html, text

dbd5ff960fd0321d74d1c995752cbe919eb14f72 Fri Mar 10 15:07:34 2023 -0800

• Committing a change that Max made some time ago to have the otto job be more resillient when panelApp is being weird. No RM.
  • src/hg/utils/otto/panelApp/genes.py - lines changed 12, context: html, text, full: html, text

c02df7dc1559b72b91e2592dbadd63ca34d3d2fb Fri Mar 10 15:09:46 2023 -0800

• Adding a change to the orphanet otto that make made a while ago but wasn't committed. Removes a field that isn't in the file any longer. No RM.
  • src/hg/utils/otto/orphanet/parseOrphadata.py - lines changed 3, context: html, text, full: html, text

821e5e9d2150d9423bc2710fc79bfaa41576f788 Fri Mar 10 15:15:51 2023 -0800

• Committing change that Max made some time ago adding additional alt/fix chroms to mastermind otto, no RM.
  • src/hg/utils/otto/mastermind/hg38/chromAlias.tab - lines changed 74, context: html, text, full: html, text

13943290b9a9a2d653074a5a59d5b3cde2bc4ecf Fri Mar 10 15:32:46 2023 -0800

• Adding a script I've had running for a while officially to the tree and under otto. This script checks the md5sums of the files in the otto git tree to the actual scripts being run on hive. Often engineers will tinker with the script directly and forget to commit their changes, because a trial period of the changes is typical. No RM.
  • src/hg/utils/otto/ottoCompareGitVsHiveFiles.py - lines changed 75, context: html, text, full: html, text

29c64e32c9e82878484db141eec2365526b32d8a Fri Mar 10 15:36:22 2023 -0800

• Adding the md5sum checker script to otto user and crontab, no RM.
  • src/hg/utils/otto/otto.crontab - lines changed 5, context: html, text, full: html, text

76abf9976eb5424081d97e0100e2f98548a4db25 Fri Mar 10 16:14:38 2023 -0800

• Adding maxWindowCoverage setting to a few tracks in RTS SNVs which take too long to load in big windows, refs #30815
  • src/hg/makeDb/trackDb/human/trackDb.clinvar.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text