2e3c89f43f3bb9d386178270200d0acce9fc8050
lrnassar
  Fri Nov 22 17:47:13 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/mouse/trackDb.ra src/hg/makeDb/trackDb/mouse/trackDb.ra
index c90e061..6c93a8a 100644
--- src/hg/makeDb/trackDb/mouse/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/trackDb.ra
@@ -40,88 +40,88 @@
 group map
 visibility hide
 type bed 4 +
 
 track gap override
 visibility hide
 
 track jaxQtl
 shortLabel MGI QTL
 longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics
 group map
 visibility hide
 color 200,100,0
 type bed 6 +
 noScoreFilter .
-url http://www.informatics.jax.org/marker/$$
+url https://www.informatics.jax.org//marker/$$
 urlLabel MGI QTL Detail: 
 
 track jaxQTL2
 shortLabel MGI QTL
 longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics
 group map
 visibility hide
 color 200,100,0
 type bed 8 +
-url http://www.informatics.jax.org/marker/$$
+url https://www.informatics.jax.org//marker/$$
 urlLabel MGI QTL Detail: 
 
 track jaxQTL3
 shortLabel MGI QTL
 longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics
 group map
 visibility hide
 color 200,100,0
 type bed 8 +
 noScoreFilter .
-url http://www.informatics.jax.org/marker/$$
+url https://www.informatics.jax.org//marker/$$
 urlLabel MGI QTL Detail: 
 
 track igtc
 shortLabel Gene Trap
 longLabel International Gene Trap Consortium Sequence Tag Alignments
 group genes 
 visibility hide
 type psl .
 url http://www.genetrap.org/cgi-bin/annotation.py?cellline=$$
 urlLabel IGTC Cell Line Annotation: 
 
 track komp
 shortLabel IKMC Genes
 longLabel International Knockout Mouse Consortium Genes
 group genes 
 visibility hide
 type bed 12
 noScoreFilter .
 itemRgb on
 urlLabel KOMP Data Coordination Center: 
 url http://www.mousephenotype.org/data/genes/$$
 mgiUrlLabel MGI Report: 
-mgiUrl http://www.informatics.jax.org/marker/$$
+mgiUrl https://www.informatics.jax.org//marker/$$
 
 track ikmc
 shortLabel IKMC Genes
 longLabel International Knockout Mouse Consortium Genes
 group genes 
 visibility hide
 type bed 12
 noScoreFilter .
 itemRgb on
 urlLabel KOMP Data Coordination Center: 
 url http://www.mousephenotype.org/data/genes/$$
 mgiUrlLabel MGI Report: 
-mgiUrl http://www.informatics.jax.org/marker/$$
+mgiUrl https://www.informatics.jax.org//marker/$$
 
 track acembly
 shortLabel AceView Genes
 longLabel AceView Gene Models With Alt-Splicing
 group genes
 visibility hide
 color 155,0,125
 type genePred acemblyPep acemblyMrna
 exonNumbers on
 autoTranslate 0
 url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&l=$$
 itemClassTbl acemblyClass
 geneClasses main putative
 gClass_main 128,0,125
 gClass_putative 200,0,125
@@ -176,67 +176,67 @@
 
     track rikenCageCtssMinus
     parent rikenCageCtss
     shortLabel Riken CAGE -
     longLabel Riken CAGE Minus Strand - Predicted Gene Start Sites
     priority 2
     color 43,51,109
 
 track jaxRepTranscript
 shortLabel MGI RepTranscrpt
 longLabel Jackson Laboratory / Mouse Genome Informatics Representative Transcript
 group phenoAllele
 visibility hide
 color 0,0,150
 type genePred
-url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=$$
+url https://www.informatics.jax.org//javawi2/servlet/WIFetch?page=markerDetail&id=$$
 urlLabel MGI Gene Detail: 
 baseColorUseCds none
 
 track jaxPhenotype
 shortLabel MGI Phenotype
 longLabel Jackson Laboratory / Mouse Genome Informatics Phenotype
 group phenoAllele
 visibility hide
 color 190,110,0
 type bed 12 +
 noScoreFilter .
-url http://www.informatics.jax.org/searches/allele_report.cgi?markerID=$$
+url https://www.informatics.jax.org//searches/allele_report.cgi?markerID=$$
 urlLabel MGI Phenotypic Allele(s): 
 
 track jaxAllele
 shortLabel MGI Allele
 longLabel Jackson Laboratory / Mouse Genome Informatics Allele
 group phenoAllele
 visibility hide
 color 200, 0, 110
 altColor 200, 0, 110
 type bed 12 +
 noScoreFilter .
-url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$
+url https://www.informatics.jax.org//javawi2/servlet/WIFetch?page=alleleDetail&id=$$
 urlLabel MGI Phenotypic Allele: 
 html jaxAlleleOld
 
 track jaxGeneTrap
 shortLabel MGI Gene Trap
 longLabel Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps
 group phenoAllele
 visibility hide
 type bed 12 +
 itemRgb on
 noScoreFilter .
-url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$
+url https://www.informatics.jax.org//javawi2/servlet/WIFetch?page=alleleDetail&id=$$
 urlLabel MGI Phenotypic Allele: 
 
 track genotypeArrays
 compositeTrack on
 shortLabel Agilent CGH
 longLabel Agilent CGH Microarray probesets
 group varRep
 visibility hide
 noInherit on
 type bed 3
 
     track agilentCgh1x1m
     parent genotypeArrays
     shortLabel Ag CGH 1x1M
     longLabel Agilent SurePrint G3 Mouse CGH Microarray 1x1M AMADID 027414