Mercurial > repos > davidvanzessen > argalaxy_tools
comparison igblast/igblast.sh @ 0:afe85eb6572e draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 29 Aug 2016 05:41:20 -0400 |
| parents | |
| children | d001d0c05dbe |
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| -1:000000000000 | 0:afe85eb6572e |
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| 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" | |
| 12 | |
| 13 java -Xmx64G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 | |
| 14 | |
| 15 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1 |