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Fix the file organisation
author Saket Choudhary <saketkc@gmail.com>
date Tue, 09 Jul 2013 14:20:26 +0530
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0:bf4b8c66fb2c 1:832a77c2ea1d
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3 This is a wrapper for a set of eQTL analysis tools.
4
5 Though, currently only PANAMA is supported.
6 PANAMA takes in input as :
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8 $panama expression_data.csv snp_data.csv
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10 Where expression_data.csv is a Comma Separated Values file containing the gene expression data
11 in the following format:
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13 sample1, sample2, ..., sampleN
14 gene1 value , value , ..., value
15 gene2 value , value , ..., value
16 ...
17 geneN
18
19 and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format:
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21 sample1, sample2, ..., sampleN
22 SNP1 value , value , ..., value
23 SNP2 value , value , ..., value
24 ...
25 SNPQ
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27 Make sure panama is installed and available on your path for all nodes.
28 Move the test-data files to your galaxy root test-data folder and
29 create a directory galaxy-central/tools/eqtl_tools and put
30 the panama_run.py and panama.xml files inside eqtl_tools directory.