Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
diff complete.sh @ 11:1b356cbde361 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 23 Jun 2015 07:52:29 -0400 |
| parents | a9053212a462 |
| children |
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--- a/complete.sh Mon Jan 12 11:07:58 2015 -0500 +++ b/complete.sh Tue Jun 23 07:52:29 2015 -0400 @@ -53,9 +53,10 @@ parsedFileName="$PWD/$parsedFileName.parsed" f=$(file $current) zipType="Zip archive" - if [[ "$f" == *"$zipType"* ]] + zxType="XZ compressed data" + if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] then - echo "<tr><td>Sample $count of patient $id is a zip file, using IMGT Loader</td></tr>" >> $html + echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html fileName=$(basename $current) imgtConvert $current $id $count $parsedFileName "${id}_${count}" #& else @@ -80,5 +81,5 @@ echo "after ED" -$dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $filterproductive +$dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" $locus $filterproductive