Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 2:4f8a1d121384 draft

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Uploaded
author davidvanzessen
date Mon, 05 Sep 2016 11:15:22 -0400
parents 90a05ff900db
children beaa487ecf43
comparison
equal deleted inserted replaced
1:90a05ff900db 2:4f8a1d121384
50 50
51 echo "<html><head><title>Report on:" >> $outputFile 51 echo "<html><head><title>Report on:" >> $outputFile
52 52
53 mkdir $outputDir/circos 53 mkdir $outputDir/circos
54 cp $dir/circos/* $outputDir/circos/ 54 cp $dir/circos/* $outputDir/circos/
55 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" 55 #CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
56 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" 56 #CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
57 57
58 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" 58 #CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
59 CIRCOSDIR="/home/galaxy/Anaconda3/bin" 59 #CIRCOSDIR="/home/galaxy/Anaconda3/bin"
60 60
61 USECIRCOS="no" 61 USECIRCOS="no"
62 if [ -d "$CIRCOSDIR" ]; then 62 if [ -d "$CIRCOSDIR" ]; then
63 USECIRCOS="yes" 63 USECIRCOS="yes"
64 else
65 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
66 USECIRCOS="yes"
67 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
68 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
69 fi
64 fi 70 fi
65 echo "Using Circos: $USECIRCOS" 71 echo "Using Circos: $USECIRCOS"
66 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf 72 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
67 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output 73 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
68 echo " $sample" >> $outputFile 74 echo " $sample" >> $outputFile