Mercurial > repos > yufei-luo > s_mart
comparison SMART/DiffExpAnal/deseq.sh @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
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| 1 #! /bin/sh | |
| 2 | |
| 3 #Arguments : | |
| 4 #$1=targetFile(the list of files) | |
| 5 #$2=with or without header | |
| 6 #$3=with or without replicates | |
| 7 #$4=OUT_HTML.html | |
| 8 #$5=OUT_HTML images directory | |
| 9 #$6=OUT_complete.xls | |
| 10 #$7=OUT_up.xls | |
| 11 #$8=OUT_down.xls | |
| 12 | |
| 13 #run example: | |
| 14 #bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls | |
| 15 | |
| 16 #echo $5 | |
| 17 #mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist. | |
| 18 | |
| 19 mkdir -p $5 | |
| 20 MY_PATH=`dirname $0` | |
| 21 cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R |