Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
view DiffExpAnal/deseq.sh @ 6:59cc55f611f6 draft
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author | yufei-luo |
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date | Tue, 22 Jan 2013 10:46:42 -0500 |
parents | 63799b789162 |
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#! /bin/sh ### ###Yufei LUO ### #Arguments : #$1=targetFile(the list of files) #$2=with or without header #$3=with or without replicates #$4=OUT_HTML.html #$5=OUT_HTML images directory #$6=OUT_complete.xls #$7=OUT_up.xls #$8=OUT_down.xls #run example: #bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls #echo $5 #mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist. mkdir -p $5 MY_PATH=`dirname $0` cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R