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                                       snpEff
                                       ------


A tool to calculate the effect of SNPs in genomes.

Main page: http://snpeff.sourceforge.net/


Galaxy install details
----------------------

  By default the snpEff is assumed to be installed in "~/snpEff", where ~ means "your home directory"
  If you install it somewhere else, you'll need to modify the following files:

	- snpEff.config:

		---------- Change data_dir param ----------
		# Interval data is stored here
		data_dir = /path/to/snpEff/data/
		---------- End of change ----------

	- snpEff.xml: This is the galaxy configuration file (in tools directory)

		---------- Change command param ----------
		<command>java -jar /path/to/snpEff/snpEff/snpEff.jar -c /path/to/snpEff/snpEff/snpEff.config $genomeVersion $input > $output</command>
		---------- End of change ----------

	WARNING!: You may need to use a custom memory value in your java virtual machine ("-XmX" option) as shown here:

		---------- Change command param ----------
		<command>java -Xmx4G -jar /path/to/snpEff/snpEff.jar -c /path/to/snpEff/snpEff.config $genomeVersion $input > $output</command>
		---------- End of change ----------

If you have any bugs, suggestions or problems, you may contact me [email protected]
Enjoy!

	Pablo Cingolani