Mercurial > repos > davidvanzessen > argalaxy_tools

comparison complete.sh @ 10:edbf4fba5fc7 draft

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Uploaded
author davidvanzessen
date Fri, 31 Jul 2015 08:08:05 -0400
parents f90fbc15b35a
children
comparison
equal deleted inserted replaced
9:079eed22fdb6 10:edbf4fba5fc7
33 count=1 33 count=1
34 continue 34 continue
35 fi 35 fi
36 echo "working on $current" 36 echo "working on $current"
37 fileName=$(basename $current) 37 fileName=$(basename $current)
38 parsedFileName="${fileName%.*}" 38 fileName="${fileName%.*}"
39 parsedFileName="$PWD/$parsedFileName.parsed" 39 parsedFileName="$PWD/$fileName.parsed"
40 f=$(file $current) 40 f=$(file $current)
41 zipType="Zip archive" 41 zipType="Zip archive"
42 zxType="XZ compressed data" 42 zxType="XZ compressed data"
43 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] 43 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
44 then 44 then
45 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html 45 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html
46 fileName=$(basename $current) 46 fileName=$(basename $current)
47 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName $count $parsedFileName "tmp" 47 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"
48 else 48 else
49 echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html 49 echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html
50 #blastAndParse $current $id $count $fileName $parsedFileName & 50 #blastAndParse $current $id $count $fileName $parsedFileName &
51 fi 51 fi
52 mergerInput+=($parsedFileName) 52 mergerInput+=($parsedFileName)