Mercurial > repos > davidvanzessen > argalaxy_tools
diff complete.sh @ 52:124b7fd92a3e draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 25 Feb 2021 13:36:15 +0000 |
| parents | d5d203d38c8a |
| children | 0ef7f80ea061 |
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--- a/complete.sh Thu Aug 08 07:40:36 2019 -0400 +++ b/complete.sh Thu Feb 25 13:36:15 2021 +0000 @@ -1,72 +1,72 @@ -#!/bin/bash -set -e -inputFiles=($1) -outputDir=$3 -outputFile=$3/index.html #$1 -clonalType=$4 -species=$5 -locus=$6 -filterproductive=$7 -clonality_method=$8 - -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 - -#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`" - -id="" -forwardSlash="/" -mergerInput=() -echo "Before loop" -count=1 -for current in "${inputFiles[@]}" -do - if [[ "$current" != *"$forwardSlash"* ]]; then - id="$current" - mergerInput+=($id) - count=1 - continue - fi - echo "working on $current" - fileName=$(basename $current) - fileName="${fileName%.*}" - parsedFileName="$PWD/$fileName.parsed" - f=$(file $current) - zipType="Zip archive" - zxType="XZ compressed data" - echo "filetype of ${id}: $f" - if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] - then - echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html - fileName=$(basename $current) - bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" - else - 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) - count=$((count+1)) -done - -echo "<tr><td>-----------------------------------</td></tr>" >> $html -echo "<tr><td>merging</td></tr>" >> $html - -bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt - -echo "<tr><td>done</td></tr>" >> $html -echo "<tr><td>-----------------------------------</td></tr>" >> $html -echo "<tr><td>plotting</td></tr>" >> $html - -echo "after ED" - -bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method - +#!/bin/bash +set -e +inputFiles=($1) +outputDir=$3 +outputFile=$3/index.html #$1 +clonalType=$4 +species=$5 +locus=$6 +filterproductive=$7 +clonality_method=$8 + +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 + +#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`" + +id="" +forwardSlash="/" +mergerInput=() +echo "Before loop" +count=1 +for current in "${inputFiles[@]}" +do + if [[ "$current" != *"$forwardSlash"* ]]; then + id="$current" + mergerInput+=($id) + count=1 + continue + fi + echo "working on $current" + fileName=$(basename $current) + fileName="${fileName%.*}" + parsedFileName="$PWD/$fileName.parsed" + f=$(file $current) + zipType="Zip archive" + zxType="XZ compressed data" + echo "filetype of ${id}: $f" + if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]] + then + echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html + fileName=$(basename $current) + bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" + else + 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) + count=$((count+1)) +done + +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>merging</td></tr>" >> $html + +bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt + +echo "<tr><td>done</td></tr>" >> $html +echo "<tr><td>-----------------------------------</td></tr>" >> $html +echo "<tr><td>plotting</td></tr>" >> $html + +echo "after ED" + +bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method +