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