File Changes for angie

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v411_base to v412_preview (2021-03-01 to 2021-03-08) v412

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src/hg/hgPhyloPlace/hgPhyloPlace.c
- lines changed 18, context: html, text, full: html, text
  68b2af5491e6f6bf71448ef639ac524823998e2a Fri Mar 5 15:27:26 2021 -0800
  Add embed & link to CDC Genomic Epi Toolkit training module for UShER.
src/hg/hgPhyloPlace/phyloPlace.c
- lines changed 35, context: html, text, full: html, text
  af86e1b9d932d0834eee1be7fe2ca77166203c48 Wed Mar 3 18:37:10 2021 -0800
  Add row of quick download links between button row and summary table.
- lines changed 45, context: html, text, full: html, text
  e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
  Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
- lines changed 26, context: html, text, full: html, text
  3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
  Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
src/hg/hgPhyloPlace/phyloPlace.h
- lines changed 3, context: html, text, full: html, text
  3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
  Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
src/hg/hgPhyloPlace/runUsher.c
- lines changed 11, context: html, text, full: html, text
  e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
  Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
- lines changed 2, context: html, text, full: html, text
  3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
  Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
src/hg/hgPhyloPlace/vcfFromFasta.c
- lines changed 2, context: html, text, full: html, text
  e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
  Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
src/hg/htdocs/covid19.html
- lines changed 12, context: html, text, full: html, text
  ec353cf62c93231178f40d06f4e7df7bfb283ee9 Fri Mar 5 15:49:19 2021 -0800
  Added link to CDC Genomic Epi Toolkit training module for UShER.
src/hg/lib/variantProjector.c
- lines changed 1, context: html, text, full: html, text
  04f1eb41233f2cd7dd80fb51f36eda1462f2899f Wed Mar 3 15:26:23 2021 -0800
  Code review feedback: ';;' --> ';'. refs #27102
src/hg/utils/faToVcf/faToVcf.c
- lines changed 20, context: html, text, full: html, text
  787bbf7122c1c5690af479fdd5639464ec7d5875 Thu Mar 4 11:26:44 2021 -0800
  Show usage message if given -h or --help. Would be nice for optionInit to take a usage function as arg so an errCatch wasn't necessary.
src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
- lines changed 1, context: html, text, full: html, text
  396fc7273c589cc83a4107a365fe67aa28b4457e Fri Mar 5 15:34:32 2021 -0800
  If BioSample date is more complete than GenBank date, use it.
src/hg/utils/otto/sarscov2phylo/getCogUk.sh
- lines changed 16, context: html, text, full: html, text
  4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
  Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
src/hg/utils/otto/sarscov2phylo/getNcbi.sh
- lines changed 4, context: html, text, full: html, text
  56405fd76d2760549a7fe511384e534f240ac79e Wed Mar 3 18:45:30 2021 -0800
  Clean up a bit when done.
- lines changed 51, context: html, text, full: html, text
  a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
  Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
- lines changed 80, context: html, text, full: html, text
  1abdb5501f3d2e51d0b48cd016c30f79bb9c12c6 Wed Mar 3 18:46:33 2021 -0800
  Run nextclade and pangolin on my manually downloaded chunks of GISAID sequences and combine them into something similar to nextmeta and nextfasta downloads.
- lines changed 1, context: html, text, full: html, text
  a6793cc4a84d4e1450fea53b558378e9f9659c64 Fri Mar 5 15:36:53 2021 -0800
  Don't need -x for this script, steps are all straightforward.
src/hg/utils/otto/sarscov2phylo/nextcladeCogUk.sh
- lines changed 26, context: html, text, full: html, text
  4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
  Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
src/hg/utils/otto/sarscov2phylo/nextcladeNcbi.sh
- lines changed 26, context: html, text, full: html, text
  a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
  Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
- lines changed 16, context: html, text, full: html, text
  a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
  Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
- lines changed 44, context: html, text, full: html, text
  7a2d50434d3fac99adc005ed3a68f9f00f92f9bf Wed Mar 3 18:43:53 2021 -0800
  Let some other script call getCogUk.sh and getNcbi.sh. Preserve ncov-ingest mappings in case of duplicates. Update local nextmeta-ish file with ID mapping when done.
src/hg/utils/otto/sarscov2phylo/updatePublic.sh
- lines changed 3, context: html, text, full: html, text
  4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
  Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
- lines changed 5, context: html, text, full: html, text
  d13f0bd04427ad790fae74040413acded3189386 Wed Mar 3 18:45:00 2021 -0800
  Call gisaidFromChunks.sh and updateIdMapping.sh to keep those up to date. Eventually will want to update GISAID+public tree.
- lines changed 3, context: html, text, full: html, text
  a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
  Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
- lines changed 10, context: html, text, full: html, text
  4e46cbfb5a3e3c506b82234e1dbb774b99bb9168 Wed Mar 3 18:42:02 2021 -0800
  Add protobufs with nextclade and pangolin annotations to public tree archive dir. Update public-latest.* links in more cgi-bin* locations. Clean up a bit.
src/inc/cheapcgi.h
- lines changed 4, context: html, text, full: html, text
  4ea1cf8aafc507f79cb6cb779e4ffb6aa6adc43f Thu Mar 4 17:48:50 2021 -0800
  Added cgiMakeOnClickButtonWithMsg for a *non*-submit button with both mouseover title and javascript.
src/lib/cheapcgi.c
- lines changed 12, context: html, text, full: html, text
  4ea1cf8aafc507f79cb6cb779e4ffb6aa6adc43f Thu Mar 4 17:48:50 2021 -0800
  Added cgiMakeOnClickButtonWithMsg for a *non*-submit button with both mouseover title and javascript.
src/utils/qa/weeklybld/userApps.sh
- lines changed 10, context: html, text, full: html, text
  7d39647272ade59ffbe565b472c53df3d7eabd80 Wed Mar 3 18:38:47 2021 -0800
  Put versioned userApps tarballs directly into the userApps.archive subdir so they are immediately available for bioconda (or other applications where a stable URL is desired).

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