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/rmskRM327.html src/hg/makeDb/trackDb/rmskRM327.html
index 883db1a..f4cc89a 100644
--- src/hg/makeDb/trackDb/rmskRM327.html
+++ src/hg/makeDb/trackDb/rmskRM327.html
@@ -1,20 +1,20 @@
 <H2>Description</H2>
 <P>
 This track was created by using a more recent version (3.2.7, Jan. 2009) 
 of Arian Smit's <A
-HREF="http://www.repeatmasker.org/"
+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, as well as a modified version of the query sequence 
 in which all the annotated repeats have been masked. RepeatMasker uses 
 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>
 Results from the original RepeatMasker run have been kept in the
 RepeatMasker track in order to avoid disrupting any analyses performed
 on the original run's results.</P>
 
@@ -48,32 +48,32 @@
 Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags
 may be used for certain organisms.  Repeats are soft-masked. Alignments may 
 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 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>