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