Mercurial > repos > davidvanzessen > argalaxy_tools
diff complete.sh @ 54:81b3eb11ed2c draft
"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
| author | rhpvorderman |
|---|---|
| date | Tue, 16 Nov 2021 15:42:32 +0000 |
| parents | 0ef7f80ea061 |
| children | 2a7dc86d8f85 |
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--- a/complete.sh Thu Feb 25 13:39:50 2021 +0000 +++ b/complete.sh Tue Nov 16 15:42:32 2021 +0000 @@ -1,6 +1,6 @@ #!/bin/bash set -e -inputFiles=($1) +inputFiles=("$1") outputDir=$3 outputFile=$3/index.html #$1 clonalType=$4 @@ -12,16 +12,16 @@ html=$2 dir="$(cd "$(dirname "$0")" && pwd)" array=("$@") -echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html -echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > "$html" +echo "<tr><td>-----------------------------------</td></tr>" >> "$html" #mkdir $PWD/igblastdatabase #unzip $dir/database.zip -d $PWD/igblastdatabase/ #export IGDATA=$PWD/igblastdatabase/ -echo "python: `which python`" -echo "R: `which R`" -echo "Rscript: `which Rscript`" +echo "python: $(which python)" +echo "R: $(which R)" +echo "Rscript: $(which Rscript)" id="" forwardSlash="/" @@ -32,15 +32,15 @@ do if [[ "$current" != *"$forwardSlash"* ]]; then id="$current" - mergerInput+=($id) + mergerInput+=("$id") count=1 continue fi echo "working on $current" - fileName=$(basename $current) + fileName=$(basename "$current") fileName="${fileName%.*}" parsedFileName="$PWD/$fileName.parsed" - f=$(file $current) + f=$(file "$current") zipType="Zip archive" zxType="XZ compressed data" echo "filetype of ${id}: $f" @@ -53,7 +53,7 @@ echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName fi - mergerInput+=($parsedFileName) + mergerInput+=("$parsedFileName") count=$((count+1)) done