Mercurial > repos > davidvanzessen > argalaxy_tools

comparison igblast/igblast.sh @ 3:c7c7000de220 draft

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author davidvanzessen
date Thu, 30 Jul 2015 09:31:38 -0400
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children c5cffbd8fe9d
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2:d8d61e65dfd5 3:c7c7000de220
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 -jar igblastwrp.jar -cf -S $species -R $locus ${input} $PWD/blasted_output
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15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1