Mercurial > repos > davidvanzessen > igblast_human

comparison igblastn.sh @ 62:a700a552f031 draft

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Uploaded
author davidvanzessen
date Wed, 20 Aug 2014 10:04:09 -0400
parents 3c52ce2256c7
children
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61:39a916965683 62:a700a552f031
1 dir="$(cd "$(dirname "$0")" && pwd)" 1 dir="$(cd "$(dirname "$0")" && pwd)"
2 echo "dir = $dir"
3 echo "pwd = $PWD"
4 mkdir $PWD/igblastdatabase 2 mkdir $PWD/igblastdatabase
5 unzip $dir/database.zip -d $PWD/igblastdatabase/ 3 unzip $dir/database.zip -d $PWD/igblastdatabase/
6 4
7 export IGDATA=$PWD/igblastdatabase/ 5 export IGDATA=$PWD/igblastdatabase/
8 6
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 7 /home/galaxy/galaxy/igblast/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