UCSC Genome Browser: Mirror Instructions

/var/www/html

rsync -navzP rsync://hgdownload.cse.ucsc.edu/gbdb/

-n, --dry-run         show what would have been transferred
-a, --archive         archive mode, equivalent to -rlptgoD
-v, --verbose         increase verbosity
-z, --compress        compress file data
-P                    equivalent to --partial --progress

#
# Executable files will be processed for SSI
#
XBitHack on

rsync -navz --progress rsync://hgdownload.cse.ucsc.edu

genome          UCSC Human Genome Downloads
htdocs          UCSC Human Genome Web Site Htdocs
goldenPath      UCSC Human Golden Path Downloads
cgi-bin         UCSC Human Genome Web Site CGI Binaries x86_64
cgi-bin-i386    UCSC Human Genome Web Site CGI Binaries i386
gbdb            UCSC Human Genome Browser Gbdb Config Files
archives        UCSC Human Genome Browser Archived Config Files
mysql           UCSC Human Genome Raw Mysql Tables

rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ $WEBROOT/

mkdir -p $WEBROOT/goldenPath/hg18/database/
rsync -avzP --delete --max-delete=20 \
  rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/hg18/database/ \
  $WEBROOT/goldenPath/hg18/database/

rsync -avzP --delete --max-delete=20 \
  rsync://hgdownload.cse.ucsc.edu/gbdb/ /gbdb/

mysql> create database $DBVERSION;

#!/bin/sh
DB=$FREEZEDATE
cd $WEBROOT/goldenPath/${DB}/database
for SQL in *.sql
do
    T_NAME=${SQL%%.sql}
    echo "loading table ${T_NAME}"
    mysql -youraccountoptions -e "DROP TABLE ${T_NAME};" ${DB} \
	> /dev/null 2> /dev/null
    mysql -youraccountoptions ${DB} < ${SQL}
    zcat "${T_NAME}.txt.gz" | mysql -youraccountoptions --local-infile=1 \
        -e "LOAD DATA LOCAL INFILE \"/dev/stdin\" INTO TABLE ${T_NAME};" ${DB}
done

mysql> grant SELECT, CREATE TEMPORARY TABLES on $DBVERSION.*
   to $USERNAME@$HOSTNAME identified by "$PASSWORD";

 rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ $CGI_BIN/ 
 rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin-i386/ $CGI_BIN/ 
setenv GLOBAL_CONFIG_FILE $CGI_BIN/hg.conf
setenv HGCGI $CGI_BIN

   mysql> create database hgcentral

   mysql -youraccountoptions hgcentral < hgcentral.sql

###########################################################
# Config file for the UCSC Human Genome server.
#	This file specifies the host and user for MySQL
#	database access.
#
# the format is in the form of name/value pairs
# written 'name=value' (note that there is no space between
# the name and its value.)
###########################################################
# db.host is the name of the MySQL host to connect to
db.host=localhost
# db.user is the username is use when connecting to the host
#	This user only needs SELECT permissions for read-only access
db.user=myhguser
# this is the password to use with the above hostname
db.password=myhguserpassword
db.trackDb=trackDb

###########################################################
# central.host is the name of the host of the central MySQL
# database where items common to all versions of the genome
# and the user database is stored.  central.db is the name of
# the database to access on that host for this information.
central.host=localhost
central.db=hgcentral
#
# The central.user needs SELECT, INSERT, UPDATE, DELETE,
#	CREATE, DROP and ALTER permissions for hgcentral
#	to allow maintainence of the session and user Db's
#
central.user=myhguser
central.password=myhguserpassword
central.domain=.mydomain.edu
###########################################################
# backupcentral is used when the primary central DB fails.
#	This can be identical to the central entries as above.
backupcentral.host=localhost
backupcentral.db=hgcentral
backupcentral.user=myhguser
backupcentral.password=myhguserpassword
backupcentral.domain=.mydomain.edu

# Change this default documentRoot if different in your installation,
#       to allow some of the browser cgi binaries to find help text
#       files
browser.documentRoot=/usr/local/apache/htdocs

#  New browser function as of March 2007, allowing saved genome browser
#       sessions into genomewiki
wiki.host=genomewiki.ucsc.edu
wiki.userNameCookie=wikidb_mw1_UserName
wiki.loggedInCookie=wikidb_mw1_UserID

# New browser function as of March 2007.  Future browser code will
#       have this on by default, and can be turned off with =off
#   Initial release of this function requires it to be turned on here.
browser.indelOptions=on

#       personalize the background of the browser with a specified jpg
#       floret.jpg is the standard UCSC default
browser.background=/images/floret.jpg
#  new option for track reording functions, August 2006
hgTracks.trackReordering=on

#  New browser function as of April 2007, custom track data is kept
#       in a database instead of in trash files.  This function requires
#       several other factors to be in place before it will work.
#  In this first implementation, this is an optional feature, but
#       approximately by the end of the year 2007, this will be
#       required.
#
#       See also:
#       http://genomewiki.ucsc.edu/index.php?title=Using_custom_track_database
#  Uncomment these settings and provide host, user, and password
#  settings
# customTracks.host=<your specific host name>
# customTracks.user=<your specific MySQL user for this function>
# customTracks.password=<MySQL password for specified user>
# customTracks.useAll=yes
# customTracks.tmpdir=/data/tmp
#       tmpdir of /data/tmp is the default location if not specified
#       here
#       Set this to a directory as recommended in the genomewiki
#       discussion mentioned above.

rsync -avzP --delete --max-delete=20 \
   rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/hgFixed/ \
   $WEBROOT/goldenPath/hgFixed/

mysql> create database hgFixed

rsync -avzP --delete --max-delete=20 \
    rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/proteinDB/ \
    $WEBROOT/goldenPath/proteinDB/

mysql> SELECT DISTINCT(proteomeDb) FROM hgcentral.gdbPdb ORDER BY proteomeDb;

mysql> create database proteins080707
mysql> create database proteins090821
and so on

	/var/lib/mysql/proteome -> proteins090821

rsync -avzP --delete --max-delete=20 \
  rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/uniProt/ \
  $WEBROOT/goldenPath/uniProt/

mysql> SHOW DATABASES LIKE 'sp%';

mysql> create database sp080707
mysql> create database sp090821
and so on

	/var/lib/mysql/uniProt  -> sp090821

rsync -avzP --delete --max-delete=20 \
   rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/visiGene/ \
   $WEBROOT/goldenPath/visiGene/

mysql> create database visiGene

4. Obtain the /gbdb data file area

5. Set up database

6. Get executable files

Change history for hgcentral database tables:

7. Set up the "hgcentral" tables

8. Create a "trash" directory

9. Create the hgFixed database

10. Create the protein databases

11. Create the UniProt databases

12. Create the visiGene database