e737f6b863c3453482f0b996b469abfc54f618c8
hiram
  Tue Apr 20 15:01:33 2021 -0700
script to update hgcentral.genark table refs #23891

diff --git src/hg/makeDb/doc/asmHubs/updateGenArkCentral.sh src/hg/makeDb/doc/asmHubs/updateGenArkCentral.sh
new file mode 100755
index 0000000..3498465
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/updateGenArkCentral.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+if [ "xxx$1" != "xxxmakeItSo" ]; then
+  printf "usage: ./updateGenArkCentral.sh makeItSo\n" 1>&2
+  printf "updates hgcentral.genark with the latest hub list from hgdownload\n" 1>&2
+  exit 255
+fi
+
+cd ~/kent/src/hg/makeDb/doc/asmHubs
+scp -p qateam@hgdownload:/mirrordata/hubs/UCSC_GI.assemblyHubList.txt ./
+
+./genArkListToSql.pl makeItSo > genark.tsv
+
+hgsql hgcentraltest -e 'drop table genark;'
+hgsql hgcentraltest < ~/kent/src/hg/lib/genark.sql
+
+hgsql hgcentraltest -e "LOAD DATA LOCAL INFILE 'genark.tsv' INTO TABLE genark;"
+
+hgsql hgcentraltest -e 'select count(*) from genark;'
+
+# +----------------+--------------+------+-----+---------+-------+
+# | Field          | Type         | Null | Key | Default | Extra |
+# +----------------+--------------+------+-----+---------+-------+
+# | gcAccession    | varchar(255) | NO   | PRI | NULL    |       |
+# | hubUrl         | varchar(255) | NO   |     | NULL    |       |
+# | asmName        | varchar(255) | NO   |     | NULL    |       |
+# | scientificName | varchar(255) | NO   |     | NULL    |       |
+# | commonName     | varchar(255) | NO   |     | NULL    |       |
+# | taxId          | int(11)      | NO   |     | NULL    |       |
+# +----------------+--------------+------+-----+---------+-------+