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comparison create_germlines.sh @ 0:dda9b2e72e2b draft

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author davidvanzessen
date Tue, 03 May 2016 09:52:21 -0400
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children 326165da9ece
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-1:000000000000 0:dda9b2e72e2b
1 #!/bin/bash
2 dir="$(cd "$(dirname "$0")" && pwd)"
3
4 input=$1
5 type=$2
6 cloned=$3
7 output=$4
8
9 cp $input $PWD/input.tab #file has to have a ".tab" extension
10
11 if [ "true" == "$cloned" ] ; then
12 cloned="--cloned"
13 else
14 cloned=""
15 fi
16
17 mkdir $PWD/outdir
18
19 #/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $germline --outdir $PWD/outdir --outname output -g $type $cloned
20 /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
21
22 mv $PWD/outdir/output_germ-pass.tab $output