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1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files
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2
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3 Installation
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4 ------------
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5
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6 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,
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7 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)
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8 2) Modify your configuration files appropriately
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9 -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
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10 -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.
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11
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12 Requirements
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13 ------------
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14 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below
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15 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided
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16
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17 ftp://ftp03.bcgsc.ca/public/rmorin/resources/
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18 (also see README.txt in that directory)
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19
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20 3) SNVMix binary version 0.12.* or later (source can be downloaded at the link provided)
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21 -follow installation instructions and put SNVMix2 binary in a location on the galaxy user's PATH
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22
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23 http://compbio.bccrc.ca/?page_id=204
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24
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25 Contacts:
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26 Rodrigo Goya for problems with SNVMix2 binary
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27 rgoya@bcgsc.ca
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28
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29 Ryan Morin for other problems
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30 rmorin@bcgsc.ca
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