Mercurial > repos > davidvanzessen > igblast_human

annotate igblastn.sh @ 60:3c52ce2256c7 draft

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author davidvanzessen
date Thu, 23 Jan 2014 07:50:56 -0500
parents 99541760fdfe
children a700a552f031
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1 dir="$(cd "$(dirname "$0")" && pwd)"
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2 echo "dir = $dir"
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3 echo "pwd = $PWD"
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4 mkdir $PWD/igblastdatabase
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5 unzip $dir/database.zip -d $PWD/igblastdatabase/
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6
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7 export IGDATA=$PWD/igblastdatabase/
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9 igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $2