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# create database
mysqladmin -u root -p create hg19

# create table
mysql -u root -p hg19 < snp142.sql

# import table entries
mysqlimport -u root -p --local hg19 snp142.txt

If you have multiple tables to download and import, use:

DBNAMES="wgEncodeAwgSegmentationSegwayGm12878 wgEncodeAwgSegmentationSegwayH1hesc wgEncodeAwgSegmentationChromhmmK562"

for DBNAME in $DBNAMES ; do
	wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/${DBNAME}.sql
	wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/${DBNAME}.txt.gz
	gzip -d ${DBNAME}.txt.gz
	mysql -u root hg19 < ${DBNAME}.sql
	mysqlimport -u root --local hg19 ${DBNAME}.txt

Windows: How to handle “Error 1290”

Without --local option, you may encounter the following error:

mysqlimport: Error: 1290, The MySQL server is running with the –secure-file-pri v option so it cannot execute this statement, when using table: snp142

Your MySQL server has been started with --secure-file-priv option which basically limits from which directories you can load files.

You may use the following commands to see the directory that has been configured.

mysql -u root -p
SHOW VARIABLES LIKE "secure_file_priv";

You have two options:

  • Move your file to the directory specified by secure-file-priv.
    • Then indicate the full paths of the txt files in the commands above.
  • Disable secure-file-priv. This must be removed from startup and cannot be modified dynamically. To do this check your MySQL start up parameters (depending on platform) and my.ini.

Ubuntu: How to change MySQL data directory

My Ubuntu disk is partitioned as below:

  • /: 32G
  • /home: 112G

By default, MySQL use /var/lib/mysql as the data directory. However, table snp142 would take about 15G and overburden /.

To solve this problem, you can change MySQL data directory. The following instructions are copied from the link in the header. Note that sudo /etc/init.d/mysql stop cannot stop mysqld; use sudo service mysql stop instead.

  1. Stop MySQL using the following command:
    • sudo service mysql stop
  2. Copy the existing data directory (default located in /var/lib/mysql) using the following command:
    • sudo cp -R -p /var/lib/mysql /[New-Path]
    • Note that the whole mysql folder would be copied to /[New-Path], making it /[New-Path]/mysql
  3. Edit the MySQL configuration file with the following command:
    • sudo gedit /etc/mysql/my.cnf
  4. Look for the entry for datadir, and change the path (which should be /var/lib/mysql) to /[New-Path]/mysql.
  5. In the terminal, enter the command:
    • sudo gedit /etc/apparmor.d/usr.sbin.mysqld
  6. Look for lines beginning with /var/lib/mysql. Change /var/lib/mysql in the lines with /[New-Path]/mysql. Save and close the file.
  7. Restart the AppArmor profiles with the command:
    • sudo /etc/init.d/apparmor reload
  8. Restart MySQL with the command:
    • sudo service mysql start