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/human/encodeEgaspUpdate.html src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
index 6318aca..ab0e231 100644
--- src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
+++ src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
@@ -4,31 +4,31 @@
 ENCODE Gene Annotation Assessment Project 
 (<A HREF="https://genome.crg.es/gencode/workshop2005.html"
 TARGET=_blank>EGASP</A>) Gene Prediction Workshop 2005.
 The following gene predictions are included:
 <UL>
 <LI>
 <A HREF="http://augustus.gobics.de/" TARGET=_blank>Augustus</A></LI>
 <LI> Exogean</LI>
 <LI>
 <A HREF="http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind"
 TARGET=_blank>FGenesh++</A></LI>
 <LI>
 <A HREF="https://genome.crg.es/software/geneid/index.html" 
 TARGET=_blank>GeneID</A>-U12 </LI>
 <LI>
-<A HREF="http://www.cbcb.umd.edu/software/jigsaw/" TARGET=_blank>Jigsaw</A></LI>
+<A HREF="https://www.cbcb.umd.edu/software/jigsaw/" TARGET=_blank>Jigsaw</A></LI>
 <LI>
 <A HREF="https://genome.crg.es/software/sgp2/index.html" 
 TARGET=_blank>SGP2</A>-U12</LI>
 <LI>
 <A HREF="http://www.pseudogenes.org" TARGET=_blank>Yale pseudogenes</A></LI>
 </UL>
 The original EGASP submissions are displayed in the companion tracks, 
 EGASP Full and EGASP Partial.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 Data for each gene prediction method within this composite annotation track 
 are displayed in separate subtracks. See the top of the track description page 
 for a complete list of the subtracks available for this annotation. To display
 only selected subtracks, uncheck the boxes next to the tracks you wish to
@@ -159,48 +159,48 @@
 <A HREF="http://gobics.de/department/" TARGET=_blank>Department of 
 Bioinformatics</A> of the University of Göttingen in Germany.</P>
 <P>
 Exogean was developed by Sarah Djebali and Hugues Roest Crollius from the
 Dyogen Lab, <A HREF="https://www.ens.psl.eu/" TARGET=_blank>Ecole 
 Normale Supérieure</A> (Paris, France) and Franck Delaplace
 from the Laboratoire de Méthodes Informatiques 
 (<A HREF="https://www.sigles.net/sigle/lami-laboratoire-des-methodes-informatiques" TARGET=_blank>LaMI</A>), (Evry, 
 France).</P>
 <P>
 The FGenesh++ gene predictions were provided by Victor Solovyev of
 <A HREF="http://www.softberry.com/" TARGET=_blank>Softberry Inc.</A>
 <P>
 The GeneID-U12 and SGP2-U12 programs were developed by the
 Grup de Recerca en Informàtica Biomèdica 
-(<A HREF="http://grib.imim.es" TARGET=_blank>GRIB</A>) at 
+(<A HREF="https://grib.upf.edu/" TARGET=_blank>GRIB</A>) at 
 the Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona.
 The version of GeneID on which GeneID-U12 is based (geneid_v1.2) was written by 
 Enrique Blanco and Roderic Guigó.
 The parameter files were constructed by Genis Parra and Francisco Camara.
 Additional contributions were made by Josep F. Abril, Moises Burset and Xavier 
 Messeguer. Modifications to GeneID that allow for the prediction of 
 U12-dependent splice sites and incorporation of U12 introns into gene models 
 were made by Tyler Alioto.</P>
 <P>
 Jigsaw was developed at The Institute for Genomic Research 
 (<A HREF="https://www.jcvi.org/" TARGET=_blank>TIGR</A>)
 by Jonathan Allen and Steven Salzberg,
 with computational gene-finder contributions from Mihaela Pertea and William 
 Majoros.  Continued maintenance and development of Jigsaw will
 be provided by the Salzberg group at the Center for Bioinformatics 
 and Computational Biology 
-(<A HREF="http://www.cbcb.umd.edu" TARGET=_blank>CBCB</A>) at the 
+(<A HREF="https://www.cbcb.umd.edu/" TARGET=_blank>CBCB</A>) at the 
 University of Maryland, College Park.</P>
 <P>
 The Yale Pseudogenes were generated by the pseudogene annotation group of 
 <A HREF="http://bioinfo.mbb.yale.edu/" TARGET=_blank>Mark Gerstein</A> at Yale 
 University.</P>
 
 <H2>References</H2>
 
 <H3>Augustus</H3>
 <P>
 Stanke, M. 
 <A HREF="https://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0006-B3F8-4"
 TARGET=_blank>Gene prediction with a hidden Markov model</A>.
 <em>Ph.D. thesis</em>, Universit&auml;t G&ouml;ttingen, Germany (2004).</P>
 <P>