src/hg/gar/garTable.sh 452b689cab327a20bb7ac506eaf89a3f69d23feb

452b689cab327a20bb7ac506eaf89a3f69d23feb
hiram
  Tue Jan 17 08:23:41 2023 -0800
invertebrates has become invertebrate and master.run.list has changed columns no redmine

diff --git src/hg/gar/garTable.sh src/hg/gar/garTable.sh
index b568d5d..8ea077c 100755
--- src/hg/gar/garTable.sh
+++ src/hg/gar/garTable.sh
@@ -1,22 +1,22 @@
 #!/bin/bash
 
 set -beEu -o pipefail
 
 export srcDir="$HOME/kent/src/hg/gar"
 
-rsync -aP hgdownload.soe.ucsc.edu::hubs/UCSC_GI.assemblyHubList.txt ./ \
+rsync -aP qateam@hgdownload.soe.ucsc.edu:/mirrordata/hubs/UCSC_GI.assemblyHubList.txt ./ \
   > /dev/null 2>&1
 
 ### starting html page output ##############################################
 printf "<!DOCTYPE HTML 4.01 Transitional>
 <!--#set var='TITLE' value='Genome assembly search and request' -->
 <!--#set var='ROOT' value='.' -->
 
 <!--#include virtual='\$ROOT/inc/gbPageStartHardcoded.html' -->
 
 <link rel='stylesheet' type='text/css' href='<!--#echo var='ROOT' -->/style/gar.css'>
 
 "
 
 # coordinate these colors with the table.pl definitions
 # export criticalColor="#ff0000"
@@ -73,31 +73,31 @@
 NCBI GenBank or RefSeq assembly accession identifier). You will be notified
 by email when your assembly is available for viewing in the UCSC Genome
 Browser. This can take up to three weeks. The assembly browser will include
 the following annotation tracks: Assembly mapping, Base position,
 Gaps, GC Percent, Restriction Enzymes, Tandem Duplications,
 CpG Islands, RefSeq mRNAs, Repeat Masking, and, if available:
 NCBI RefSeq Genes and Ensembl Genes.
 </p>
 <p>This page is optimized for use in Firefox and Safari.
 </p>
 <p>For more details on using this page, please see this <a href='https://genome-blog.soe.ucsc.edu/blog/2022/04/12/genark-hubs-part-4/' target=_blank>blog post</a>.
 </p>\n"
 
 grep -v "^#" \
   /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/master.run.list \
-    | cut -d' ' -f3,5 | awk '{printf "%s\t%s\n", $1, $2};' | sort -k1,1 -u \
+    | cut -d' ' -f2,4 | awk '{printf "%s\t%s\n", $1, $2};' | sort -k1,1 -u \
        > asmId.sciName
 
 ls /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \
   | grep -v others.orderList.tsv | xargs grep -h -v "^#" | sort -k1,1 -u \
     > asmId.commonName;
 
 sort -u /hive/data/outside/ncbi/genomes/reports/newAsm/*.suppressed.asmId.list \
   > asmId.suppressed.list
 
 join -t$'\t' asmId.sciName asmId.commonName > asmId.sciName.commonName
 
 $srcDir/garTable.pl
 
 # the column 1 tooltip display window, controlled in javaScript
 printf "<div id='col1ToolTip' class='col1ToolTip'>request</div>\n"