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diff complete.sh @ 53:0ef7f80ea061 draft

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Uploaded
author davidvanzessen
date Thu, 25 Feb 2021 13:39:50 +0000
parents 124b7fd92a3e
children 81b3eb11ed2c
line wrap: on
line diff
--- a/complete.sh	Thu Feb 25 13:36:15 2021 +0000
+++ b/complete.sh	Thu Feb 25 13:39:50 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
+