From 322f5e8960bbed25be8e731c3f075259255568fd Mon Sep 17 00:00:00 2001
From: Niklas Reimer <n.reimer@uni-luebeck.de>
Date: Tue, 16 Nov 2021 11:27:37 +0100
Subject: [PATCH] add ucsc to panel and tumor only

---
 make_panel_report.sh     | 2 +-
 make_tumorOnly_report.sh | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/make_panel_report.sh b/make_panel_report.sh
index be9ab0d..806df8d 100755
--- a/make_panel_report.sh
+++ b/make_panel_report.sh
@@ -81,7 +81,7 @@ ${BIN_RSCRIPT} "${DIR_RSCRIPT}/Main.R" "${CFG_CASE}" "${PARAM_DIR_PATIENT}" "${C
   "${DIR_TARGET}" "${DIR_RSCRIPT}" "${DIR_DATABASE}" "${CFG_REFERENCE_CAPTUREGENES}" "${CFG_REFERENCE_COVEREDREGION}" \
   "${CFG_AUTHOR}" "${CFG_CENTER}" "${CFG_REFERENCE_CAPTUREREGIONS}" "${CFG_REFERENCE_CAPTUREREGIONNAME}" "${FILE_GENOME}" \
   "${CFG_REFERENCE_CAPTURECORFACTORS}" "${CFG_PANEL_MINVAF}" "${CFG_VARSCAN_PANEL_FPFILTER_MINVARCOUNT}" "${CFG_GENERAL_MAFCUTOFF}" \
-  "${CFG_REFERENCE_ACTIONABLEGENES}" "${CFG_REFERENCE_COVERED_EXONS}"
+  "${CFG_REFERENCE_ACTIONABLEGENES}" "${CFG_REFERENCE_COVERED_EXONS}" "${CFG_UCSC_SERVER}"
 
 # translate to tex
 ${BIN_RSCRIPT} --vanilla -e "load('${DIR_ANALYSES}/MTB.RData'); library(knitr); knit('${DIR_RSCRIPT}/Report_Panel.Rnw');"
diff --git a/make_tumorOnly_report.sh b/make_tumorOnly_report.sh
index 6c02743..5729e51 100755
--- a/make_tumorOnly_report.sh
+++ b/make_tumorOnly_report.sh
@@ -75,7 +75,7 @@ ${BIN_RSCRIPT} "${DIR_RSCRIPT}/Main.R" "${CFG_CASE}" "${PARAM_DIR_PATIENT}" "${C
   "${DIR_TARGET}" "${DIR_RSCRIPT}" "${DIR_DATABASE}" "${CFG_REFERENCE_CAPTUREGENES}" "${CFG_REFERENCE_COVEREDREGION}" \
   "${CFG_AUTHOR}" "${CFG_CENTER}" "${CFG_REFERENCE_CAPTUREREGIONS}" "${CFG_REFERENCE_CAPTUREREGIONNAME}" "${FILE_GENOME}" \
   "${CFG_REFERENCE_CAPTURECORFACTORS}" "${CFG_VARSCAN_MINVAF}" "${CFG_VARSCAN_FPFILTER_MINVARCOUNT}" "${CFG_GENERAL_MAFCUTOFF}" \
-  "${CFG_REFERENCE_ACTIONABLEGENES}" "${CFG_REFERENCE_COVERED_EXONS}"
+  "${CFG_REFERENCE_ACTIONABLEGENES}" "${CFG_REFERENCE_COVERED_EXONS}" "${CFG_UCSC_SERVER}"
 
 # translate to tex
 ${BIN_RSCRIPT} --vanilla -e "load('${DIR_ANALYSES}/MTB.RData'); library(knitr); knit('${DIR_RSCRIPT}/Report_tumorOnly.Rnw');"