Mercurial > repos > davidvanzessen > change_o
diff create_germlines.sh @ 0:183edf446dcf draft default tip
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| author | davidvanzessen |
|---|---|
| date | Mon, 17 Jul 2017 07:44:27 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_germlines.sh Mon Jul 17 07:44:27 2017 -0400 @@ -0,0 +1,23 @@ +#!/bin/bash +dir="$(cd "$(dirname "$0")" && pwd)" + +input=$1 +type=$2 +cloned=$3 +output=$4 + +cp $input $PWD/input.tab #file has to have a ".tab" extension + +if [ "true" == "$cloned" ] ; then + cloned="--cloned" +else + cloned="" +fi + +mkdir $PWD/outdir + +#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +#/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +python3 $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned + +mv $PWD/outdir/output_germ-pass.tab $output