Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data

comparison deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/deseq.sh @ 10:6e573fd3c41b draft

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author yufei-luo
date Mon, 13 May 2013 10:06:30 -0400
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9:a03838a6eb54 10:6e573fd3c41b
1 #! /bin/sh
2 ###
3 ###Yufei LUO
4 ###
5
6
7 #Arguments :
8 #$1=targetFile(the list of files)
9 #$2=with or without header
10 #$3=with or without replicates
11 #$4=OUT_HTML.html
12 #$5=OUT_HTML images directory
13 #$6=OUT_complete.xls
14 #$7=OUT_up.xls
15 #$8=OUT_down.xls
16
17 #run example:
18 #bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls
19
20 #echo $5
21 #mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist.
22
23 mkdir -p $5
24 MY_PATH=`dirname $0`
25 cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R