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comparison change_o/define_clones.sh @ 72:c787e79e8b90 draft

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Uploaded
author davidvanzessen
date Tue, 05 Feb 2019 03:26:41 -0500
parents c33d93683a09
children aff3ba86ef7a
comparison
equal deleted inserted replaced
71:2649a821162d 72:c787e79e8b90
19 link=$8 19 link=$8
20 dist=$9 20 dist=$9
21 output=${10} 21 output=${10}
22 output2=${11} 22 output2=${11}
23 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 24 DefineClones.py -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 25
28 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 26 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
29 else 27 else
30 method=$3 28 method=$3
31 output=$4 29 output=$4
32 output2=$5 30 output2=$5
33 31
34 python3 $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method 32 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 33
38 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 34 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
39 fi 35 fi
40 36
41 cp $PWD/outdir/output_clone-pass.tab $output 37 cp $PWD/outdir/output_clone-pass.tab $output