Mercurial > repos > rhpvorderman > shm_csr

annotate change_o/define_clones.sh @ 0:64d74ba01a7c draft

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"planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
author rhpvorderman
date Wed, 27 Oct 2021 12:34:47 +0000
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1 #!/bin/bash
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2 # something to make it commit, with unix line ends
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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5 #define_clones.sh $input $noparse $scores $regions $out_file
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7 type=$1
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8 input=$2
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9
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10 mkdir -p $PWD/outdir
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12 cp $input $PWD/input.tab #file has to have a ".tab" extension
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14 if [ "bygroup" == "$type" ] ; then
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15 mode=$3
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16 act=$4
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17 model=$5
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18 norm=$6
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19 sym=$7
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20 link=$8
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21 dist=$9
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22 output=${10}
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23 output2=${11}
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25 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
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27 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
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28 else
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29 method=$3
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30 output=$4
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31 output2=$5
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33 DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method
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35 Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1
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36 fi
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38 cp $PWD/outdir/output_clone-pass.tab $output
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40 rm -rf $PWD/outdir/