Friday, October 09, 2009

load ucsc hg19 into mysql database

at /common/data/finishedwork/public_databases/hg19
wget --timestamping -r -l 1 --no-parent --no-directories -A"sql" ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database
ls -l *.sql|cut -c 51-|sed s/\.sql/\.txt\.gz/>gz.lst
wget --timestamping --no-directories -i gz.lst --base=ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
cat *.sql>sql.script
/common/software/mysql/bin/mysql -htiger -uzhibin -p ucsc_hg19<sql.script
/common/software/mysql/bin/mysqlimport -htiger -uzhibin -p --local -v ucsc_hg19 *.txt</sql.script

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