Mercurial > repos > davidvanzessen > argalaxy_tools

annotate igblast/igblast.sh @ 2:4f8a1d121384 draft

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author davidvanzessen
date Mon, 05 Sep 2016 11:15:22 -0400
parents afe85eb6572e
children d001d0c05dbe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 set -e
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2
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4
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5 input=$1
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6 species=$2
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7 locus=$3
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8 output=$4
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11 echo "$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
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15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1