Mercurial > repos > davidvanzessen > igblast_human

comparison igblastn.sh @ 60:3c52ce2256c7 draft

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Uploaded
author davidvanzessen
date Thu, 23 Jan 2014 07:50:56 -0500
parents 99541760fdfe
children a700a552f031
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59:76df2ddba956 60:3c52ce2256c7
2 echo "dir = $dir" 2 echo "dir = $dir"
3 echo "pwd = $PWD" 3 echo "pwd = $PWD"
4 mkdir $PWD/igblastdatabase 4 mkdir $PWD/igblastdatabase
5 unzip $dir/database.zip -d $PWD/igblastdatabase/ 5 unzip $dir/database.zip -d $PWD/igblastdatabase/
6 6
7 export IGDATA=$PWD/igblastdatabase/
8
7 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 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