# HG changeset patch # User davidvanzessen # Date 1390554153 18000 # Node ID 6364030a16b86f79ccb0472859f396050e66ae3a # Parent 364b169ffb30903732c8721fa8d7f5a9436929ec Uploaded diff -r 364b169ffb30 -r 6364030a16b8 combined.sh --- a/combined.sh Thu Jan 23 08:30:59 2014 -0500 +++ b/combined.sh Fri Jan 24 04:02:33 2014 -0500 @@ -1,10 +1,5 @@ #!/bin/bash -mkdir $PWD/igblastdatabase -unzip $dir/database.zip -d $PWD/igblastdatabase/ - -export IGDATA=$PWD/igblastdatabase/ - clonalType=${@:(-3):1} html=${@:(-2):1} imageDir=${@:(-1):1} @@ -15,7 +10,9 @@ echo "

Progress

" > $html echo "" >> $html - +mkdir $PWD/igblastdatabase +unzip $dir/database.zip -d $PWD/igblastdatabase/ +export IGDATA=$PWD/igblastdatabase/ function blastAndParse { echo "" >> $html
info
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Starting blast of sample $3 of patient $2