Mercurial > repos > davidvanzessen > argalaxy_tools
comparison complete.sh @ 12:010402c959aa draft
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| author | davidvanzessen |
|---|---|
| date | Tue, 04 Aug 2015 10:00:20 -0400 |
| parents | |
| children | cf1def1aaa74 |
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| 11:0510cf1f7cbc | 12:010402c959aa |
|---|---|
| 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 | |
| 13 html=$2 | |
| 14 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 15 array=("$@") | |
| 16 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html | |
| 17 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 18 | |
| 19 #mkdir $PWD/igblastdatabase | |
| 20 #unzip $dir/database.zip -d $PWD/igblastdatabase/ | |
| 21 #export IGDATA=$PWD/igblastdatabase/ | |
| 22 | |
| 23 id="" | |
| 24 forwardSlash="/" | |
| 25 mergerInput=() | |
| 26 echo "Before loop" | |
| 27 count=1 | |
| 28 for current in "${inputFiles[@]}" | |
| 29 do | |
| 30 if [[ "$current" != *"$forwardSlash"* ]]; then | |
| 31 id="$current" | |
| 32 mergerInput+=($id) | |
| 33 count=1 | |
| 34 continue | |
| 35 fi | |
| 36 echo "working on $current" | |
| 37 fileName=$(basename $current) | |
| 38 fileName="${fileName%.*}" | |
| 39 parsedFileName="$PWD/$fileName.parsed" | |
| 40 f=$(file $current) | |
| 41 zipType="Zip archive" | |
| 42 zxType="XZ compressed data" | |
| 43 if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] | |
| 44 then | |
| 45 echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html | |
| 46 fileName=$(basename $current) | |
| 47 bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" | |
| 48 else | |
| 49 echo "<tr><td>Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn</td></tr>" >> $html | |
| 50 bash ${dir}/igblast/igblast.sh $current $species $locus $parsedFileName | |
| 51 fi | |
| 52 mergerInput+=($parsedFileName) | |
| 53 count=$((count+1)) | |
| 54 done | |
| 55 wait | |
| 56 | |
| 57 echo "after loop" | |
| 58 | |
| 59 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 60 echo "<tr><td>merging</td></tr>" >> $html | |
| 61 | |
| 62 python $dir/experimental_design/experimental_design.py ${mergerInput[*]} --output $PWD/merged.txt | |
| 63 | |
| 64 echo "<tr><td>done</td></tr>" >> $html | |
| 65 echo "<tr><td>-----------------------------------</td></tr>" >> $html | |
| 66 echo "<tr><td>plotting</td></tr>" >> $html | |
| 67 | |
| 68 echo "after ED" | |
| 69 | |
| 70 bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method | |
| 71 |