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comparison define_clones.sh @ 6:3ddd933dd7a2 draft default tip

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author davidvanzessen
date Thu, 15 Sep 2016 03:54:33 -0400
parents 6f57d43a1f4c
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5:3d97839fda21 6:3ddd933dd7a2
4 #define_clones.sh $input $noparse $scores $regions $out_file 4 #define_clones.sh $input $noparse $scores $regions $out_file
5 5
6 type=$1 6 type=$1
7 input=$2 7 input=$2
8 8
9 mkdir $PWD/outdir 9 mkdir -p $PWD/outdir
10
11 echo "defineclones: $PWD/outdir"
10 12
11 cp $input $PWD/input.tab #file has to have a ".tab" extension 13 cp $input $PWD/input.tab #file has to have a ".tab" extension
12 14
13 if [ "bygroup" == "$type" ] ; then 15 if [ "bygroup" == "$type" ] ; then
14 mode=$3 16 mode=$3
19 link=$8 21 link=$8
20 dist=$9 22 dist=$9
21 output=${10} 23 output=${10}
22 output2=${11} 24 output2=${11}
23 25
24 /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 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 #/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 #/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
26 28
27 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 29 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
28 else 30 else
29 method=$3 31 method=$3
30 output=$4 32 output=$4
31 output2=$5 33 output2=$5
32 34
33 /data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method 35 python3 $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
34 #/home/galaxy/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
35 37
36 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 38 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
37 fi 39 fi
38 40