Mercurial > repos > davidvanzessen > argalaxy_tools

comparison igblast/igblast.sh @ 46:4d2a8f98a502 draft

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Uploaded
author davidvanzessen
date Mon, 28 Jan 2019 09:37:41 -0500
parents 8cbc1a8d27ae
children e35b82f31ec7
comparison
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45:942eea8359fe 46:4d2a8f98a502
22 fi 22 fi
23 23
24 echo "$input $species $locus $output" 24 echo "$input $species $locus $output"
25 25
26 java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1 26 java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
27 #java -Xmx64G -jar $dir/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
28 #java -Xmx64G -jar $dir/migmap-1.0.1.jar -p 4 -S "$species" -R $locus ${input} $PWD/blasted_output 2>&1
29 27
30 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1 28 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1