68b2af5491e6f6bf71448ef639ac524823998e2a
angie
  Fri Mar 5 15:27:26 2021 -0800
Add embed & link to CDC Genomic Epi Toolkit training module for UShER.

diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c
index 1c5c27c..9b3daef 100644
--- src/hg/hgPhyloPlace/hgPhyloPlace.c
+++ src/hg/hgPhyloPlace/hgPhyloPlace.c
@@ -177,30 +177,48 @@
      "target=_blank>China National Center for Bioinformation</a>), "
      "and your sequence's placement in the phylogenetic tree generated by the\n"
      "<a href='https://github.com/roblanf/sarscov2phylo' target='_blank'>sarscov2phylo</a>\n"
      "pipeline.\n"
      "Placement is performed by\n"
      "<a href='https://github.com/yatisht/usher' target=_blank>"
      "Ultrafast Sample placement on Existing tRee (UShER)</a> "
      "(<a href='https://www.biorxiv.org/content/10.1101/2020.09.26.314971v1' target=_blank>"
      "Turakhia <em>et al.</em></a>).  UShER also generates local subtrees to show samples "
      "in the context of the most closely related sequences.  The subtrees can be visualized "
      "as Genome Browser custom tracks and/or using "
      "<a href='https://nextstrain.org' target=_blank>Nextstrain</a>'s interactive display "
      "which supports "
      "<a href='"NEXTSTRAIN_DRAG_DROP_DOC"' "
      "target=_blank>drag-and-drop</a> of local metadata that remains on your computer.</p>\n");
+puts("</div>");
+puts("</div>");
+puts("<div class='readableWidth'>");
+puts("<div class='gbControl col-md-12'>\n"
+     "<div style='float:left; margin-right: 10px;'>"
+     "<iframe width='267' height='150' src='https://www.youtube.com/embed/humQ1NyZOUM' frameborder='0' allow='accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture' allowfullscreen></iframe>\n"
+     "</div><p>"
+     "The <a href='https://www.cdc.gov/amd/training/covid-19-gen-epi-toolkit.html' target=_blank>"
+     "CDC COVID-19 Genomic Epidemiology Toolkit</a> now includes a training module for UShER!\n"
+     "Module 3.3 includes a <a href='https://youtu.be/humQ1NyZOUM' target=_blank>video</a>, "
+     "slides (<a href='https://www.cdc.gov/amd/pdf/slidesets/toolkit-module-3.3-usher.pdf' "
+     "target=_blank>PDF</a>), and links to more resources.\n"
+     "</p>"
+     );
+puts("</div>");
+puts("</div>");
+puts("<div class='readableWidth'>");
+puts("  <div class='gbControl col-md-12'>");
 puts("<p><b>Note:</b> "
      "Please do not upload any files that contain "
      "<a href='https://en.wikipedia.org/wiki/Protected_health_information#United_States' "
      "target=_blank>Protected Health Information (PHI)</a> "
      "to UCSC.</p>\n"
      "<p>We do not store your information "
      "(aside from the information necessary to display results)\n"
      "and will not share it with others unless you choose to share your Genome Browser view.</p>\n"
      "<p>In order to enable rapid progress in SARS-CoV-2 research and genomic contact tracing,\n"
      "please share your SARS-CoV-2 sequences by submitting them to an "
      "<a href='https://ncbiinsights.ncbi.nlm.nih.gov/2020/08/17/insdc-covid-data-sharing/' "
      "target=_blank>INSDC</a> member institution\n"
      "(<a href='https://submit.ncbi.nlm.nih.gov/sarscov2/' target=_blank>NCBI</a>,\n"
      "<a href='https://www.covid19dataportal.org/submit-data' target=_blank>EMBL-EBI</a>\n"
      "or <a href='https://www.ddbj.nig.ac.jp/ddbj/websub.html' target=_blank>DDBJ</a>)\n"