Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 1:90a05ff900db draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 05 Sep 2016 04:46:06 -0400 |
| parents | afe85eb6572e |
| children | 4f8a1d121384 |
| files | report_clonality/RScript.r report_clonality/circos/LTe50046.ttf report_clonality/circos/LTe50048.ttf report_clonality/circos/LTe50050.ttf report_clonality/circos/LTe50054.ttf report_clonality/circos/circos.tar.gz report_clonality/circos/pragmata.ttf report_clonality/circos/wingding.ttf report_clonality/r_wrapper.sh |
| diffstat | 9 files changed, 7 insertions(+), 0 deletions(-) [+] |
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--- a/report_clonality/RScript.r Mon Aug 29 05:41:20 2016 -0400 +++ b/report_clonality/RScript.r Mon Sep 05 04:46:06 2016 -0400 @@ -115,6 +115,9 @@ clonalityFrame = clonalityFrame[!duplicated(clonalityFrame$clonality_clonaltype), ] } +print("SAMPLE TABLE:") +print(table(PRODF$Sample)) + prod.unique.sample.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample")]) prod.unique.rep.count = data.frame(data.table(PRODF)[, list(Productive_unique=.N), by=c("Sample", "Replicate")])
--- a/report_clonality/r_wrapper.sh Mon Aug 29 05:41:20 2016 -0400 +++ b/report_clonality/r_wrapper.sh Mon Sep 05 04:46:06 2016 -0400 @@ -54,6 +54,10 @@ cp $dir/circos/* $outputDir/circos/ CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" + +CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" +CIRCOSDIR="/home/galaxy/Anaconda3/bin" + USECIRCOS="no" if [ -d "$CIRCOSDIR" ]; then USECIRCOS="yes"