Mercurial > repos > davidvanzessen > argalaxy_tools
view igblast/igblast.sh @ 6:d001d0c05dbe draft
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author | davidvanzessen |
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date | Fri, 16 Dec 2016 07:30:32 -0500 |
parents | afe85eb6572e |
children | 54f6756bacb1 |
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set -e dir="$(cd "$(dirname "$0")" && pwd)" input=$1 species=$2 locus=$3 output=$4 declare -A speciesdict speciesdict=(["Bos taurus functional"]="BosTaurus" ["Bos taurus non-functional"]="BosTaurus" ["Camelus dromedarius functional"]="CamelusDromedarius" ["Camelus dromedarius non-functional"]="CamelusDromedarius" ["Canis lupus familiaris functional"]="CanisLupusFamiliaris" ["Canis lupus familiaris non-functional"]="CanisLupusFamiliaris" ["Danio rerio non-functional"]="DanioRerio" ["Danio rerio functional"]="DanioRerio" ["Homo sapiens functional"]="HomoSapiens" ["Homo sapiens non-functional"]="HomoSapiens" ["Macaca mulatta non-functional"]="MacacaMulatta" ["Macaca mulatta functional"]="MacacaMulatta" ["Mus musculus functional"]="MusMusculus" ["Mus musculus non-functional"]="MusMusculus" ["Mus spretus functional"]="MusSpretus" ["Mus spretus non-functional"]="MusSpretus" ["Oncorhynchus mykiss functional"]="OncorhynchusMykiss" ["Oncorhynchus mykiss non-functional"]="OncorhynchusMykiss" ["Oryctolagus cuniculus functional"]="OryctolagusCuniculus" ["Oryctolagus cuniculus non-functional"]="OryctolagusCuniculus" ["Rattus norvegicus functional"]="RattusNorvegicus" ["Rattus norvegicus non-functional"]="RattusNorvegicus" ["Sus scrofa functional"]="SusScrofa" ["Sus scrofa non-functional"]="SusScrofa" ["BosTaurus"]="BosTaurus" ["CamelusDromedarius"]="CamelusDromedarius" ["CanisLupusFamiliaris"]="CanisLupusFamiliaris" ["DanioRerio"]="DanioRerio" ["HomoSapiens"]="HomoSapiens" ["MacacaMulatta"]="MacacaMulatta" ["MusMusculus"]="MusMusculus" ["MusSpretus"]="MusSpretus" ["OncorhynchusMykiss"]="OncorhynchusMykiss" ["OryctolagusCuniculus"]="OryctolagusCuniculus" ["RattusNorvegicus"]="RattusNorvegicus" ["SusScrofa"]="SusScrofa") echo "$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