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/nestedRepeatsRM327.html src/hg/makeDb/trackDb/nestedRepeatsRM327.html
index d27d2a2..2c5b188 100644
--- src/hg/makeDb/trackDb/nestedRepeatsRM327.html
+++ src/hg/makeDb/trackDb/nestedRepeatsRM327.html
@@ -1,20 +1,20 @@
 <H2>Description</H2>
 <P>
 This track shows joined fragments of interrupted repeats extracted from 
 the output of a more recent version (3.2.7, Jan. 2009) of the
-<A HREF="http://www.repeatmasker.org/"
+<A HREF="https://www.repeatmasker.org/"
 TARGET=_blank>RepeatMasker</A> program, which screens DNA sequences 
 for interspersed repeats and low complexity DNA sequences using 
 the <A HREF="https://www.girinst.org/repbase/update/index.html"
 TARGET=_blank>Repbase Update</A> library of repeats from the 
 <A HREF="https://www.girinst.org/" TARGET=_blank>Genetic 
 Information Research Institute</A> (GIRI).  
 Repbase Update is described in Jurka, J. (2000) in the References section below.
 </P>
 <P>
 The detailed annotations from RepeatMasker are in the RepMask 3.2.7
 track.  This track shows fragments of original repeat insertions 
 which have been
 interrupted by insertions of younger repeats or through local
 rearrangements.  The fragments are joined using the ID column of
 RepeatMasker output.
@@ -50,32 +50,32 @@
 </P>
 <P>
 Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags
 may be used for certain organisms.  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 and Green, P. RepeatMasker Open-3.0.
-<A HREF="http://www.repeatmasker.org" 
-TARGET=_BLANK>http://www.repeatmasker.org</A>. 1996-2007.
+<A HREF="https://www.repeatmasker.org/" 
+TARGET=_BLANK>https://www.repeatmasker.org/</A>. 1996-2007.
 </P>
 <P>
 Repbase Update is described in 
 Jurka J. 
 <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10973072"
 TARGET=_blank>Repbase update: a database and an electronic journal of 
 repetitive elements</A>. 
 <em>Trends Genet</em>. 2000 Sep;16(9):418-420.</P>
 <P>
 For a discussion of repeats in mammalian genomes, see: 
 <P>
 Smit AF. <A HREF="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10607616"
 TARGET=_blank>Interspersed repeats and other mementos of transposable 
 elements in mammalian genomes</A>. <em>Curr Opin Genet Dev</em>. 1999 Dec;9(6):
 657-63.</P>