Mercurial > repos > ryanmorin > nextgen_variant_identification

diff SNV/README @ 6:361d6506850a

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author ryanmorin
date Tue, 18 Oct 2011 18:32:07 -0400
parents 74f5ea818cea
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--- a/SNV/README	Mon Oct 17 14:57:09 2011 -0400
+++ b/SNV/README	Tue Oct 18 18:32:07 2011 -0400
@@ -3,8 +3,11 @@
 Installation
 ------------
 
-1) Place these files in $GALAXY_HOME/tools
-2) Modify your configuration files appropriately, for example, add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section)
+1) Place these files in $GALAXY_HOME/tools and compile/install SNVMix2 if you haven't already done so (also copy/link the SNVMix2 binary, 
+identify_nonsynonymous_mutations.pl and filter_snvmix.pl to /usr/local/bin or some other location in the default PATH, also ensure they are executable)
+2) Modify your configuration files appropriately
+-add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section), see the tool_conf.xml.sample for an example
+-create or modify $GALAXY_HOME/sam_fa_indices.loc to match the example provided (points galaxy to the fasta files containing the genome that was used during the alignment step).  These are needed by SNVMix.
 
 Requirements
 ------------