Mercurial > repos > davidvanzessen > argalaxy_tools

comparison complete.sh @ 24:d5d203d38c8a draft

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Uploaded
author davidvanzessen
date Wed, 01 Feb 2017 09:48:38 -0500
parents 54f6756bacb1
children 124b7fd92a3e
comparison
equal deleted inserted replaced
23:e2fbdfacec1d 24:d5d203d38c8a
17 17
18 #mkdir $PWD/igblastdatabase 18 #mkdir $PWD/igblastdatabase
19 #unzip $dir/database.zip -d $PWD/igblastdatabase/ 19 #unzip $dir/database.zip -d $PWD/igblastdatabase/
20 #export IGDATA=$PWD/igblastdatabase/ 20 #export IGDATA=$PWD/igblastdatabase/
21 21
22 echo "python: `which python`"
23 echo "R: `which R`"
24 echo "Rscript: `which Rscript`"
25
22 id="" 26 id=""
23 forwardSlash="/" 27 forwardSlash="/"
24 mergerInput=() 28 mergerInput=()
25 echo "Before loop" 29 echo "Before loop"
26 count=1 30 count=1
37 fileName="${fileName%.*}" 41 fileName="${fileName%.*}"
38 parsedFileName="$PWD/$fileName.parsed" 42 parsedFileName="$PWD/$fileName.parsed"
39 f=$(file $current) 43 f=$(file $current)
40 zipType="Zip archive" 44 zipType="Zip archive"
41 zxType="XZ compressed data" 45 zxType="XZ compressed data"
46 echo "filetype of ${id}: $f"
42 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] 47 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
43 then 48 then
44 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html 49 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html
45 fileName=$(basename $current) 50 fileName=$(basename $current)
46 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" 51 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"