Mercurial > repos > davidvanzessen > argalaxy_tools

comparison igblast/igblast.sh @ 5:bcec7bb4e089 draft

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Uploaded
author davidvanzessen
date Mon, 12 Dec 2016 05:22:57 -0500
parents afe85eb6572e
children d001d0c05dbe
comparison
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4:5ffd52fc35c4 5:bcec7bb4e089
1 set -e
2
3 dir="$(cd "$(dirname "$0")" && pwd)"
4
5 input=$1
6 species=$2
7 locus=$3
8 output=$4
9
10
11 echo "$input $species $locus $output"
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13 java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
14
15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1