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view igblast/igblast.sh @ 3:beaa487ecf43 draft

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author davidvanzessen
date Wed, 07 Dec 2016 08:36:23 -0500
parents afe85eb6572e
children d001d0c05dbe
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set -e

dir="$(cd "$(dirname "$0")" && pwd)"

input=$1
species=$2
locus=$3
output=$4


echo "$input $species $locus $output"

java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1

Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1