Mercurial > repos > davidvanzessen > argalaxy_tools

comparison igblast/igblast.sh @ 8:8cbc1a8d27ae draft

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Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 08:50:31 -0500
parents 54f6756bacb1
children 4d2a8f98a502
comparison
equal deleted inserted replaced
7:54f6756bacb1 8:8cbc1a8d27ae
13 13
14 echo "Species: $species ${speciesdict[$species]}" 14 echo "Species: $species ${speciesdict[$species]}"
15 15
16 species="${speciesdict[$species]}" 16 species="${speciesdict[$species]}"
17 17
18 if [ "$species" == "" ]
19 then
20 >&2 echo "Species not possible with igBLASTn, use IMGT"
21 exit 1
22 fi
23
18 echo "$input $species $locus $output" 24 echo "$input $species $locus $output"
19 25
20 java -Xmx64G -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
21 #java -Xmx64G -jar $dir/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
22 #java -Xmx64G -jar $dir/migmap-1.0.1.jar -p 4 -S "$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
23 29
24 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1 30 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1