Mercurial > repos > davidvanzessen > argalaxy_tools
diff complete.sh @ 10:edbf4fba5fc7 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 31 Jul 2015 08:08:05 -0400 |
| parents | f90fbc15b35a |
| children |
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--- a/complete.sh Thu Jul 30 10:00:08 2015 -0400 +++ b/complete.sh Fri Jul 31 08:08:05 2015 -0400 @@ -35,8 +35,8 @@ fi echo "working on $current" fileName=$(basename $current) - parsedFileName="${fileName%.*}" - parsedFileName="$PWD/$parsedFileName.parsed" + fileName="${fileName%.*}" + parsedFileName="$PWD/$fileName.parsed" f=$(file $current) zipType="Zip archive" zxType="XZ compressed data" @@ -44,7 +44,7 @@ then echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html fileName=$(basename $current) - bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName $count $parsedFileName "tmp" + bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" else echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html #blastAndParse $current $id $count $fileName $parsedFileName &