add ucsc to panel and tumor only

AG-Boerries · Nov 16, 2021 · 322f5e8 · 322f5e8
1 parent 1241ff5
commit 322f5e8
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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');"