Mercurial > repos > davidvanzessen > argalaxy_tools
comparison complete.sh @ 0:afe85eb6572e draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 29 Aug 2016 05:41:20 -0400 |
| parents | |
| children | 54f6756bacb1 |
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| -1:000000000000 | 0:afe85eb6572e |
|---|---|
| 1 #!/bin/bash | |
| 2 set -e | |
| 3 inputFiles=($1) | |
| 4 outputDir=$3 | |
| 5 outputFile=$3/index.html #$1 | |
| 6 clonalType=$4 | |
| 7 species=$5 | |
| 8 locus=$6 | |
| 9 filterproductive=$7 | |
| 10 clonality_method=$8 | |
| 11 | |
| 12 html=$2 | |
| 13 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 14 array=("$@") | |
| 15 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html | |
| 16 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 17 | |
| 18 #mkdir $PWD/igblastdatabase | |
| 19 #unzip $dir/database.zip -d $PWD/igblastdatabase/ | |
| 20 #export IGDATA=$PWD/igblastdatabase/ | |
| 21 | |
| 22 id="" | |
| 23 forwardSlash="/" | |
| 24 mergerInput=() | |
| 25 echo "Before loop" | |
| 26 count=1 | |
| 27 for current in "${inputFiles[@]}" | |
| 28 do | |
| 29 if [[ "$current" != *"$forwardSlash"* ]]; then | |
| 30 id="$current" | |
| 31 mergerInput+=($id) | |
| 32 count=1 | |
| 33 continue | |
| 34 fi | |
| 35 echo "working on $current" | |
| 36 fileName=$(basename $current) | |
| 37 fileName="${fileName%.*}" | |
| 38 parsedFileName="$PWD/$fileName.parsed" | |
| 39 f=$(file $current) | |
| 40 zipType="Zip archive" | |
| 41 zxType="XZ compressed data" | |
| 42 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] | |
| 43 then | |
| 44 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html | |
| 45 fileName=$(basename $current) | |
| 46 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" | |
| 47 else | |
| 48 echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html | |
| 49 bash ${dir}/igblast/igblast.sh $current $species $locus $parsedFileName | |
| 50 fi | |
| 51 mergerInput+=($parsedFileName) | |
| 52 count=$((count+1)) | |
| 53 done | |
| 54 | |
| 55 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 56 echo "<tr><td>merging</td></tr>" >> $html | |
| 57 | |
| 58 bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt | |
| 59 | |
| 60 echo "<tr><td>done</td></tr>" >> $html | |
| 61 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 62 echo "<tr><td>plotting</td></tr>" >> $html | |
| 63 | |
| 64 echo "after ED" | |
| 65 | |
| 66 bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method | |
| 67 |