8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
  Fri Nov 15 18:50:19 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

diff --git src/hg/makeDb/trackDb/joinedRmsk.html src/hg/makeDb/trackDb/joinedRmsk.html
index 45d4a55..6f49523 100644
--- src/hg/makeDb/trackDb/joinedRmsk.html
+++ src/hg/makeDb/trackDb/joinedRmsk.html
@@ -1,20 +1,20 @@
 <h2>Description</h2>
 
 <p>
 This track was created using Arian Smit's
-<a href="http://www.repeatmasker.org/" target="_blank">RepeatMasker</a>
+<a href="https://www.repeatmasker.org/" target="_blank">RepeatMasker</a>
 program, which screens DNA sequences
 for interspersed repeats and low complexity DNA sequences. The program
 outputs a detailed annotation of the repeats that are present in the
 query sequence (represented by this track), as well as a modified version
 of the query sequence in which all the annotated repeats have been masked
 (generally available on the
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html"
 target=_blank>Downloads</a> page). RepeatMasker uses a separately curated version of the 
 <a href="https://www.girinst.org/repbase/update/index.html"
 target=_blank>Repbase Update</a> repeat library from the
 <a href="https://www.girinst.org/" target=_blank>Genetic 
 Information Research Institute</a> (GIRI).
 Repbase Update is described in Jurka (2000) in the References section below.  </p>
 <p>
 Alternatively, RepeatMasker can use the new
@@ -411,32 +411,32 @@
 extend through repeats, but are not permitted to initiate in them.
 See the <a href="/FAQ/FAQdownloads#download16">FAQ</a> for more information.
 </p>
 
 <h2>Credits</h2>
 
 <p>
 Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and
 repeat libraries used to generate this track.
 </p>
 
 <h2>References</h2>
 
 <p>
 Smit AFA, Hubley R, Green P. <em>RepeatMasker Open-3.0</em>.
-<a href="http://www.repeatmasker.org" target="_blank">
-http://www.repeatmasker.org</a>. 1996-2010.
+<a href="https://www.repeatmasker.org/" target="_blank">
+https://www.repeatmasker.org/</a>. 1996-2010.
 </p>
 
 <p>
 Dfam is described in:
 </p>
 <p>
 Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.
 <a href="https://academic.oup.com/nar/article/41/D1/D70/1073076/Dfam-a-database-of-repetitive-DNA-
 based-on-profile" target="_blank">
 Dfam: a database of repetitive DNA based on profile hidden Markov models</a>.
 <em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D70-82.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23203985" target="_blank">23203985</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531169/" target="_blank">PMC3531169</a>
 </p>