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/sacCer/multizYeast.html src/hg/makeDb/trackDb/sacCer/multizYeast.html
index f133c71..7cdfe3a 100644
--- src/hg/makeDb/trackDb/sacCer/multizYeast.html
+++ src/hg/makeDb/trackDb/sacCer/multizYeast.html
@@ -1,31 +1,31 @@
 <H2>Description</H2> 
 <P>
 This track shows a measure of evolutionary conservation in seven species of
 the genus <em>Saccharomyces</em> based on a phylogenetic hidden Markov model
 (phastCons).  The graphic display shows the alignment projected onto
 <em>S. cerevisiae</em>. 
 <P>
 The genomes were downloaded from:<BR>
 <UL>
 <LI><em>S. cerevisiae</em> - <A HREF="https://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/" TARGET=_blank>http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/</A>
 <LI><em>S. paradoxus</em> - <A HREF="ftp://ftp.broadinstitute.org/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Spar_contigs.fasta" TARGET=_blank>http://www.broadinstitute.org/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Spar_contigs.fasta</A>
 <LI><em>S. mikatae</em> - <A HREF="ftp://ftp.broadinstitute.org/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Smik_contigs.fasta" TARGET=_blank>http://www.broadinstitute.org/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Smik_contigs.fasta</A>
-<LI><em>S. kudriavzevii</em> - <A HREF="http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz" TARGET=_blank>http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz</A>
+<LI><em>S. kudriavzevii</em> - <A HREF="https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz" TARGET=_blank>https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM6553.fsa.gz</A>
 <LI><em>S. bayanus</em> - <A HREF="ftp://ftp.broadinstitute.org/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Sbay_contigs.fasta" TARGET=_blank>http://www.broadinstitute.org/ftp/pub/annotation/fungi/comp_yeasts/S1a.Assembly/Sbay_contigs.fasta</A>
-<LI><em>S. castelli</em> - <A HREF="http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz" TARGET=_blank>http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz</A>
-<LI><em>S. kluyveri</em> - <A HREF="http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz" TARGET=_blank>http://www.genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz</A>
+<LI><em>S. castelli</em> - <A HREF="https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz" TARGET=_blank>https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM476.fsa.gz</A>
+<LI><em>S. kluyveri</em> - <A HREF="https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz" TARGET=_blank>https://genetics.wustl.edu/saccharomycesgenomes/Contigs/YM479.fsa.gz</A>
 </UL>
 </P>
 <P>
 In full display mode, this track shows the overall conservation score across all
 species as well as pairwise alignments 
 of each species with <em>$Organism</em>.  The pairwise alignments are
 shown in dense display mode using a grayscale 
 density gradient.  The checkboxes in the track configuration section allow
 the exclusion of species from the pairwise display; however, this does not
 remove them from the conservation score display.  </P>
 <P>
 When zoomed-in to the base-display level, the track shows the base 
 composition of each alignment. The numbers and symbols on the Gaps
 line indicate the lengths of gaps in the <em>$Organism</em> sequence at those 
 alignment positions relative to the longest non-<em>$Organism</em> sequence.