Commits for angie

v409_base to v410_preview (2021-01-18 to 2021-01-25) v410

466fc186d05dd8e8bd27f91752bcb03d8edd63a6 Tue Jan 19 11:03:38 2021 -0800

• Add try/except to prevent some encoding problem when writing varPaths from crashing the script.
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 4, context: html, text, full: html, text

83eb31f4ea1896449dce8576697627091c6ff313 Thu Jan 21 10:54:13 2021 -0800

• Prevent excess warnings about varPaths problems.
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 4, context: html, text, full: html, text

4be38ba46f1cc49a9ac3dd60719bcf824aef8a0b Thu Jan 21 10:55:34 2021 -0800

• Tweak: use set -x in order to see which command fails when there's a silent failure (e.g. from wget -q).
  • src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 1, context: html, text, full: html, text

c36ffe3e1a45ff7977ebb772b0fdc937fe37bf9f Fri Jan 22 10:54:25 2021 -0800

• Add Nextstrain clade coloring for sarsCov2PhyloPub, release alpha only until the coloring file is pushed.
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 51, context: html, text, full: html, text

2a551773f1cca84e8acb73cf1856f78111d53002 Fri Jan 22 10:57:17 2021 -0800

• Use curl not wget to avoid annoying .1, .2 files on retries.
  • src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 4, context: html, text, full: html, text

40960dac74599ef433b17978620bcc4ec06e8d08 Fri Jan 22 10:58:13 2021 -0800

• Update coloring for recently added Nextstrain clades; accept any letter for Pangolin lineages.
  • src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl - lines changed 12, context: html, text, full: html, text

c8d7abe94b3244702501b71b62d9e1ea6333228b Sat Jan 23 14:24:20 2021 -0800

• Grab COG-UK daily tree as Russ suggests; might want to try using it instead of GISAID tree.
  • src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 1, context: html, text, full: html, text

562a5ca722b958707b6ac1033d5dec067da96736 Sat Jan 23 14:25:01 2021 -0800

• Add source ~/.bashrc at beginning. Not sure why that was not necessary before but is now.
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 1, context: html, text, full: html, text

4e6b762738442dc4fc6a2a9c38618cf7bae7da44 Sat Jan 23 14:26:09 2021 -0800

• David request: replace "variant" with "mutation" because virologists & the press often use "variant" the way we would use "strain". Where I was previously using "SNV" to highlight that our Phylogeny tracks use only SNVs not indels, I now use "nucleotide substitution".
  • src/hg/makeDb/trackDb/virus/wuhCor1/lineageB_1_1_7_US.html - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainParsimony.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/problematicSites.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPubParsimony.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 22, context: html, text, full: html, text