Mercurial > repos > davidvanzessen > argalaxy_tools

diff complete.sh @ 0:afe85eb6572e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 29 Aug 2016 05:41:20 -0400
parents
children 54f6756bacb1
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/complete.sh	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,67 @@
+#!/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/
+
+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 $current)
+	zipType="Zip archive"
+	zxType="XZ compressed data"
+  	if [[ "$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
+