Mercurial > repos > davidvanzessen > change_o
view create_germlines.sh @ 2:6f57d43a1f4c draft
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author | davidvanzessen |
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date | Thu, 11 Aug 2016 07:40:36 -0400 |
parents | 326165da9ece |
children | 3ddd933dd7a2 |
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#!/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 mv $PWD/outdir/output_germ-pass.tab $output