Mercurial > repos > davidvanzessen > argalaxy_tools

comparison igblast/igblast.sh @ 12:010402c959aa draft

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author davidvanzessen
date Tue, 04 Aug 2015 10:00:20 -0400
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children dca3273a7291
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11:0510cf1f7cbc 12:010402c959aa
1 set -e
2
3 dir="$(cd "$(dirname "$0")" && pwd)"
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5 input=$1
6 species=$2
7 locus=$3
8 output=$4
9
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11 echo "$input $species $locus $output"
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13 java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -cf -S $species -R $locus ${input} $PWD/blasted_output 2>&1
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15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1