7072384d5e6f4228bec4186d3d677527be0c9bc5
mspeir
  Fri Jun 26 09:37:20 2026 -0700
Adding data access to hs1 pages on the RR, refs #

diff --git src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html
index 0dcf7dab418..acf2717d085 100644
--- src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html
+++ src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html
@@ -1,44 +1,61 @@
 <h2>Description</h2>
 <p>
   Cactus reference-free alignments of GRCh38 and T2T CHM13 v2.0, using chimp
   (GCF_002880755.1/panTro6) as an out-group.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
   This track uses the <a href="/goldenPath/help/hgTracksHelp.html#SnakeDisplay">Snake tracks</a> display conventions and configuration.
 </p>
 
 <h2>Methods</h2>
 <p>
   Alignments were generated using the Cactus reference alignment package and are stored
   as a HAL file.
 </p>
 
+<h2>Data Access</h2>
+<p>
+The alignment summary can be explored interactively with the
+<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>.</p>
+<p>
+The full multiple alignment is stored as a HAL file that can be downloaded from our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/hgCactus/" target="_blank">download server</a> as
+<tt>t2tChm13.v2.0.hal</tt>. HAL files can be queried and converted with the tools in the
+<a href="https://github.com/ComparativeGenomicsToolkit/hal" target="_blank">HAL toolkit</a>.</p>
+<p>
+Please refer to our
+<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing
+list archives</a> for questions, or our
+<a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more
+information.</p>
+
 <h2>Credits</h2>
 <p>
   This track was created by <a href="mhauknes@ucsc.edu"> Marina Haukness &lt;mhauknes@ucsc.edu&gt;</a>
   if the UC Santa Cruz Computational Genomics Lab.
 </p>
 
 <h2>References</h2>
 <p>
 Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J
 <em>et al</em>.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank">
 Progressive Cactus is a multiple-genome aligner for the thousand-genome era</a>.
 <em>Nature</em>. 2020 Nov;587(7833):246-251.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank">33177663</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673649/" target="_blank">PMC7673649</a>
 </p>
 <p>
 Hickey G, Paten B, Earl D, Zerbino D, Haussler D.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/23505295" target="_blank">
 HAL: a hierarchical format for storing and analyzing multiple genome alignments</a>.
 <em>Bioinformatics</em>. 2013 May 15;29(10):1341-2.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23505295" target="_blank">23505295</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707/" target="_blank">PMC3654707</a>
 </p>