Mercurial > repos > davidvanzessen > igblastn_immunerepertoire_igg
diff combined.sh @ 1:7b0d9c107680 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jan 2014 08:29:40 -0500 |
| parents | d52f6a986108 |
| children | 364b169ffb30 |
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--- a/combined.sh Thu Jan 23 08:22:28 2014 -0500 +++ b/combined.sh Thu Jan 23 08:29:40 2014 -0500 @@ -1,6 +1,9 @@ #!/bin/bash -#export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0; +mkdir $PWD/igblastdatabase +unzip $dir/database.zip -d $PWD/igblastdatabase/ + +export IGDATA=$PWD/igblastdatabase/ clonalType=${@:(-3):1} html=${@:(-2):1} @@ -12,10 +15,12 @@ echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html echo "<tr><td>-----------------------------------</td></tr>" >> $html + + function blastAndParse { echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html echo "$IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4" - $IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4 + $IGDATA/bin/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 > $PWD/$4 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html