Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 2:4f8a1d121384 draft
Uploaded
author | davidvanzessen |
---|---|
date | Mon, 05 Sep 2016 11:15:22 -0400 (2016-09-05) |
parents | 90a05ff900db |
children | beaa487ecf43 |
files | report_clonality/circos/fonts.conf report_clonality/r_wrapper.sh |
diffstat | 2 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/report_clonality/circos/fonts.conf Mon Sep 05 04:46:06 2016 -0400 +++ b/report_clonality/circos/fonts.conf Mon Sep 05 11:15:22 2016 -0400 @@ -1,8 +1,8 @@ -default = fonts/LTe50046.ttf -normal = fonts/LTe50046.ttf -bold = fonts/LTe50048.ttf -condensed = fonts/LTe50050.ttf -condensedbold = fonts/LTe50054.ttf -mono = fonts/pragmata.ttf -glyph = fonts/wingding.ttf +default = LTe50046.ttf +normal = LTe50046.ttf +bold = LTe50048.ttf +condensed = LTe50050.ttf +condensedbold = LTe50054.ttf +mono = pragmata.ttf +glyph = wingding.ttf
--- a/report_clonality/r_wrapper.sh Mon Sep 05 04:46:06 2016 -0400 +++ b/report_clonality/r_wrapper.sh Mon Sep 05 11:15:22 2016 -0400 @@ -52,15 +52,21 @@ mkdir $outputDir/circos cp $dir/circos/* $outputDir/circos/ -CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" -CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" +#CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" +#CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" -CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" -CIRCOSDIR="/home/galaxy/Anaconda3/bin" +#CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" +#CIRCOSDIR="/home/galaxy/Anaconda3/bin" USECIRCOS="no" if [ -d "$CIRCOSDIR" ]; then USECIRCOS="yes" +else + if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix + USECIRCOS="yes" + CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" + CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" + fi fi echo "Using Circos: $USECIRCOS" sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf