976c0e681fc3571f3a449ee2f7cb78400f11ce3e
markd
  Fri Jul 22 11:39:18 2022 -0700
moved t2t-supplied tracks out of bbi

diff --git src/hg/makeDb/doc/hs1/t2t-supplied.txt src/hg/makeDb/doc/hs1/t2t-supplied.txt
index 845a0e9..413394e 100644
--- src/hg/makeDb/doc/hs1/t2t-supplied.txt
+++ src/hg/makeDb/doc/hs1/t2t-supplied.txt
@@ -1,34 +1,45 @@
 T2T project supplied tracks for T2T-CHM13v2.0
 
 Note that some of these instructions were originally done for the GenArk
-promoted hub.  These files were then copied over.  This maybe result in some
-of the file paths being incorrect.
+promoted hub.  These files were then copied over and this text edited.
+However, they were not rebuilt, so this maybe result in some of the file paths
+being incorrect.
+
+T2T CHM13 track spreadsheet:
+
+   https://docs.google.com/spreadsheets/d/13BXuEFB904aje6zWXyZ0znZnXvQiu1qxKADA2uV2JU4/
+
 
 The following bash function is used to link files to /gbdb/hs1/bbi that include
 that track directory.  Must call in the form
+
    lngbdb censat/censat.bb 
 
 lngbdb() {
    local bb gdir
    for bb in $* ; do
-      gdir=/gbdb/hs1/bbi/$(dirname $bb)
+      gdir=/gbdb/hs1/$(dirname $bb)
       mkdir -p $gdir
       ln -s $(realpath $bb) $gdir/
     done
 }
 
+# to use hubCheck
+
+   hubCheck /gbdb/hs1/hubs/$USER/hub.txt 
+
 ================================================================
 proseq (2022-02-21 markd)
 ----------------------------------------------------------------
 Supplied by Savannah Hoyt <savannah.klein@uconn.edu>
 from T2T Globus /team-epigenetics/PROseq-RNAseq_chm13v1.1/MappedToCHM13v1.1/PROseq_Bowtie2/
 trackData/proseq
 
 renaming files to something not as long
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-chm13v1.1_neg.bigwig                              -> PROseq_default_neg.bw
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-chm13v1.1_pos.bigwig                              -> PROseq_default_pos.bw
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_meryl-21mer-chm13v1.1_neg.bigwig   -> PROseq_k100_21mer_neg.bw
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_meryl-21mer-chm13v1.1_pos.bigwig   -> PROseq_k100_21mer_pos.bw
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_neg.bigwig                         -> PROseq_k100_neg.bw
     CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_pos.bigwig                         -> PROseq_k100_pos.bw
     PROseq_k100_AB.markersandlength_meryl-21mer-chm13v1.1_neg.bigwig                                 -> PROseq_k100_dual_21mer_neg.bw
@@ -367,15 +378,19 @@
     # Convert to bigRmskBed and bigRmskAlignBed files
     /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskAlignBed.as -type=bed3+14  combo.align.tsv.sorted chrom.sizes chm13v2.0_RMSK_ALIGN.bb
     /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskBed.as -type=bed9+5 combo.join.tsv.sorted chrom.sizes chm13v2.0_RMSK.bb
 
 2022-05-23
 # due to the number of problems with the bigRmsk code, we are temporarily converting it to
 # a bigBed and added colors.
 
   cd /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/trackData/t2tRepeatMasker
   bigBedToBed chm13v2.0_rmsk.align.bb stdout |  awk -f addItemRgb.awk >chm13v2.0_rmsk.align.rgb.bed
 
 
 lngbdb t2tRepeatMasker/*.bb
 
 ================================================================
+Problems:
+- hub groups doesn't have phenDis, so put clinvar and GWAS in varRep
+  FIX THIS
+================================================================