Elementolab/Cancer Exome Mutation Discovery pipeline

Ole2001 — Sun, 19 May 2013 15:53:15 GMT

/* Loading mutations into the cBio portal */

Revision as of 15:53, 19 May 2013		Current revision
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-	Login and load data	+	Login and load data:
	ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com		ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com
	cd $PORTAL_HOME/core/src/main/scripts		cd $PORTAL_HOME/core/src/main/scripts
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	sudo /etc/init.d/tomcat6 stop		sudo /etc/init.d/tomcat6 stop
	sudo /etc/init.d/tomcat6 start		sudo /etc/init.d/tomcat6 start
		+
		+	To load CNAs: (data_CNA.txt being matrix of +1, 0, -1 etc for each gene, typically generated by GISTIC)
		+	$PORTAL_HOME/core/src/main/scripts/importProfileData.pl --data $PORTAL_DATA_HOME/studies/baca/data_CNA.txt \
		+	--meta $PORTAL_DATA_HOME/studies/baca/meta_CNA.txt --dbmsAction clobber
		+

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