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comparison change_o/define_clones.sh @ 0:8a5a2abbb870 draft default tip

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author davidvanzessen
date Mon, 29 Aug 2016 05:36:10 -0400
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-1:000000000000 0:8a5a2abbb870
1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 #define_clones.sh $input $noparse $scores $regions $out_file
5
6 type=$1
7 input=$2
8
9 mkdir -p $PWD/outdir
10
11 cp $input $PWD/input.tab #file has to have a ".tab" extension
12
13 if [ "bygroup" == "$type" ] ; then
14 mode=$3
15 act=$4
16 model=$5
17 norm=$6
18 sym=$7
19 link=$8
20 dist=$9
21 output=${10}
22 output2=${11}
23
24 python3 $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
25 #/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
26 #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link
27
28 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
29 else
30 method=$3
31 output=$4
32 output2=$5
33
34 python3 $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
35 #/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
36 #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
37
38 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
39 fi
40
41 cp $PWD/outdir/output_clone-pass.tab $output
42
43 rm -rf $PWD/outdir/