e1e7a65c65869e5b0d157cd1e992e8c905157524
markd
  Sun Apr 25 22:01:45 2021 -0700
added Zoonomia phylop subtrack

diff --git src/hg/makeDb/doc/hg38/cactus241way.txt src/hg/makeDb/doc/hg38/cactus241way.txt
index f0fcdc2..48805f9 100644
--- src/hg/makeDb/doc/hg38/cactus241way.txt
+++ src/hg/makeDb/doc/hg38/cactus241way.txt
@@ -1,16 +1,40 @@
 #########################################################################
+# Zoonomia phyloP for 241-way from (2021-04-24 MarkD)
+
+  cd /hive/data/genomes/hg38/bed/cactus241way/phyloP
+
+  # Obtain phylogP scores computed by Michael Dong (Uppsala U).  Since Broad
+  # has had their ftp and http sharing of files turned off, they were placed
+  # in google drive (LoL)
+
+  # download from https://drive.google.com/drive/u/0/folders/1Xc215oxu0cvBZOarxFv2L3HAjPmiZ-0A
+  # to directory uppsala
+
+  # format is, so convert with awk
+  chr1	10074	10075	id-1	0.053000
+  chr1	10075	10076	id-2	0.064000
+  chr1	10076	10077	id-3	0.064000
+
+  # convert to wig and wib
+  zcat uppsala/chr*.bed.gz  | tawk '{print $1,$2,$3,$5}' | wigEncode stdin phyloP241way.wig phyloP241way.wib
+
+  ln -s $(pwd)/phyloP241way.wib /gbdb/hg38/cactus241way/
+  hgLoadWiggle -pathPrefix=/gbdb/hg38/cactus241way hg38 phyloP241way phyloP241way.wig 
+
+
+########################################################################
 # phastCons 241-way (TBD - 2015-05-07 - Hiram)
     # split 241way mafs into 10M chunks and generate sufficient statistics
     # files for # phastCons
     ssh ku
     mkdir -p /hive/data/genomes/hg38/bed/cactus241way/cons/ss
     mkdir -p /hive/data/genomes/hg38/bed/cactus241way/cons/msa.split
     cd /hive/data/genomes/hg38/bed/cactus241way/cons/msa.split
 
     cat << '_EOF_' > doSplit.csh
 #!/bin/csh -ef
 set c = $1
 set MAF = /hive/data/genomes/hg38/bed/cactus241way/ucscNames/$c.maf
 set WINDOWS = /hive/data/genomes/hg38/bed/cactus241way/cons/ss/$c
 set WC = `cat $MAF | wc -l`
 set NL = `grep "^#" $MAF | wc -l`
@@ -679,31 +703,31 @@
     cd /hive/data/genomes/hg38/bed/cactus241way/downloads/phyloP241way
 
     mkdir hg38.241way.phyloP
     cd hg38.241way.phyloP
 
     ln -s ../../../consPhyloP/all/downloads/*.wigFix.gz .
     md5sum *.wigFix.gz > md5sum.txt
 
     cd ..
 
     ln -s ../../consPhyloP/run.phyloP/all.mod hg38.phyloP241way.mod
     ln -s ../../consPhyloP/all/phyloP241way.bw hg38.phyloP241way.bw
 
     md5sum *.mod *.bw > md5sum.txt
 
-    # obtain the README.txt from hg38/phyloP20way and update for this
+    # Obtain The README.txt from hg38/phyloP20way and update for this
     mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP241way/hg38.241way.phyloP
     cd hg38.241way.phyloP
     ln -s `pwd`/* \
 /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP241way/hg38.241way.phyloP
 
     cd ..
 
     #   situation
     ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/phyloP241way
 
 #############################################################################
 # hgPal downloads (TBD - 2017-11-06 - Hiram)
 #   FASTA from 241-way for ncbiRefSeq, refGene and knownCanonical