Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 12:5f5d29c5e711 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 10:03:41 -0500
parents 8cbc1a8d27ae
children 21ca9391a3b7
comparison
equal deleted inserted replaced
11:607f176350bf 12:5f5d29c5e711
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 64 else
65 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix 65 if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix
66 USECIRCOS="yes" 66 USECIRCOS="yes"
67 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" 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/" 68 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
69 fi 69 fi
70 fi 70
71 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
72 USECIRCOS="yes"
73 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
74 CIRCOSDIR="/home/galaxy/Anaconda3/bin"
75 fi
76 fi
77
71 echo "Using Circos: $USECIRCOS" 78 echo "Using Circos: $USECIRCOS"
72 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf 79 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
73 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output 80 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
74 echo " $sample" >> $outputFile 81 echo " $sample" >> $outputFile
75 82