Commits for hiram

v393_base to v394_preview (2020-01-27 to 2020-02-03) v394

ea79a1e6a7795f886789c87decc48cd89646fa2e Mon Jan 27 14:28:39 2020 -0800

• destination directory for symlinks is now in a new location refs #24354
  • src/hg/makeDb/doc/globalReference/mkSymLinks.sh - lines changed 35, context: html, text, full: html, text

a59176fe95d3fc8f34a2988f6086f33da509925d Tue Jan 28 14:19:33 2020 -0800

• adding legal statement to liftOver/README.txt file no redmine
  • src/hg/utils/automation/makeDownloads.pl - lines changed 15, context: html, text, full: html, text

1f2373cd5d35b4cb3db0ee2497380d7844cb3266 Wed Jan 29 11:19:54 2020 -0800

• coronavirus viron schematic from Belouzard, et al. Viruses. 2012 Jun; 4(6): 1011-1033
  • src/hg/htdocs/images/2019-nCoV.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

8bbc807db3bfb9774c93264c0167ac129239b624 Wed Jan 29 11:32:51 2020 -0800

• not all NCBI fields may be defined refs #24851
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 19, context: html, text, full: html, text

9093f0d4ffd8ea540c1244f9ff899b97faddd260 Wed Jan 29 11:55:41 2020 -0800

• beginning build of wuhCor1 browser
  • src/hg/makeDb/doc/wuhCor1/initialBuild.txt - lines changed 1240, context: html, text, full: html, text

dafc38a60fa78a7a14bfaf05905e2190da48a386 Wed Jan 29 12:17:10 2020 -0800

• correctly avoid trying to remove something that does not exist refs #24851
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 2, context: html, text, full: html, text

46235f87089ef4defc1b576e1fad0b2aefa6d05c Wed Jan 29 14:25:10 2020 -0800

• adding wuhCor1 to the build refs #24851
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/gap.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 26, context: html, text, full: html, text

23fe352f0fecf53c475eab36afb881e57aa59f8a Wed Jan 29 14:31:52 2020 -0800

• nearing completion refs #24851
  • src/hg/makeDb/doc/wuhCor1/initialBuild.txt - lines changed 492, context: html, text, full: html, text

4944d96d31a51aae682fea89155ab91165b3c9c3 Wed Jan 29 14:44:07 2020 -0800

• eliminate the geneDesc table reference and correct assembly reference for the photo refs #24851
  • src/hg/makeDb/trackDb/virus/wuhCor1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

a9a452d3405a1d32a6a4f0e71ec02cdd70792d1a Thu Jan 30 11:32:13 2020 -0800

• add definitions for wuhCor1 refs #24851
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text

04737fb7f583ed3168dc5594e0cb8403efccd911 Thu Jan 30 17:18:50 2020 -0800

• protect against zero results refs #23891
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 16, context: html, text, full: html, text

623b6e9bb69c43d27321823c079d9367582c75e9 Thu Jan 30 17:19:40 2020 -0800

• add rmskSpecies argument and protect against empty xenoRefGene result refs #23891
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 10, context: html, text, full: html, text

2e901bb19e96fbe3fe8bb9706cf528a20ed2477d Thu Jan 30 17:20:19 2020 -0800

• protect against empty nestedRepeats result refs #23891
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 4, context: html, text, full: html, text

a87c21c0843e05386bc8539b11305e8aa0439a44 Thu Jan 30 17:21:01 2020 -0800

• verify all required input files are available refs #23891
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 15, context: html, text, full: html, text

137d847d5d74037f32026ad75a55d219c2abbb1f Thu Jan 30 17:21:31 2020 -0800

• protect against empty result refs #23891
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 12, context: html, text, full: html, text

56bd05da3e479f71dc7f90fe1293bcd67ddc1775 Fri Jan 31 14:11:44 2020 -0800

• initial view of ClinGen composite track refs #24818
  • src/hg/makeDb/trackDb/human/hg19/doseSensitivity.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text