Mercurial > repos > davidvanzessen > argalaxy_tools
diff igblast/igblast.sh @ 5:bcec7bb4e089 draft
Uploaded
author | davidvanzessen |
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date | Mon, 12 Dec 2016 05:22:57 -0500 |
parents | afe85eb6572e |
children | d001d0c05dbe |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igblast/igblast.sh Mon Dec 12 05:22:57 2016 -0500 @@ -0,0 +1,15 @@ +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