improving prerequisite checking

broadinstitute · Jun 28, 2018 · f14af73 · f14af73
1 parent 17ac3b1
commit f14af73
Show file tree

Hide file tree

Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/scripts/sv/evaluation/general/misc_functions.sh b/scripts/sv/evaluation/general/misc_functions.sh
@@ -47,6 +47,11 @@ else
         exit 1
 fi
 
+command -v bedtools >/dev/null 2>&1 || { echo >&2 "I require bedtools for interval intersection analysis but it's not installed. Aborting."; exit 1; }
+command -v R >/dev/null 2>&1 || { echo >&2 "I require R but it's not installed. Aborting."; exit 1; }
+temp=$(Rscript -e 'packages <-c("stringr", "plyr");  uninstalled <- packages[ which(packages %in% installed.packages()[, "Package"]==F) ]; uninstalled')if [[ $ALL_RPACK_INSTALLED == "FALSE" ]]; then
+if [[ $temp != "character(0)" ]]; then echo "Required R package(s) $temp not installed; Aborting."; exit 1; fi
+
 ########## get primary contigs pattern given requested assembly version (must be 19 or 38)
 function get_primary_contigs_pattern() {
     PRIMARY_CONTIGS_PATTERN=""

diff --git a/scripts/sv/evaluation/manage/AccountingAndPrep/checkAndParseGATK.sh b/scripts/sv/evaluation/manage/AccountingAndPrep/checkAndParseGATK.sh
@@ -35,8 +35,8 @@ echo " Delegating to R for producing plots"
 echo 
 
 CURR_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-Rscript "$CURR_DIR/plotInsDelSizes.R" "$ANALYSIS_DIR_MASTER" "$MANTA_AND_PACBIO_PREANALYSIS_DIR"
-Rscript "$CURR_DIR/plotInsDelSizes.R" "$ANALYSIS_DIR_FEATURE" "$MANTA_AND_PACBIO_PREANALYSIS_DIR"
+Rscript "$CURR_DIR/plotInsDelSizes.R" "$ANALYSIS_DIR_MASTER" "$MANTA_AND_PACBIO_PREANALYSIS_DIR" "$SCRIPT_DIR"
+Rscript "$CURR_DIR/plotInsDelSizes.R" "$ANALYSIS_DIR_FEATURE" "$MANTA_AND_PACBIO_PREANALYSIS_DIR" "$SCRIPT_DIR"
 
 echo 
 echo " Done producing plots"

diff --git a/scripts/sv/evaluation/manage/AccountingAndPrep/plotInsDelSizes.R b/scripts/sv/evaluation/manage/AccountingAndPrep/plotInsDelSizes.R
@@ -2,7 +2,6 @@
 # and deletion calls
 
 #########################################################################
-source("../../general/AccountingAndPrep/func_collectSizes.R")
 
 args<-commandArgs(TRUE)
 wd <- args[1]
@@ -12,6 +11,10 @@ print(paste("working in directory", wd))
 
 mantaAndPacBioDir <- args[2]
 
+scriptDir <- args[3]
+helperPath <- paste0(scriptDir, "AccountingAndPrep/func_collectSizes.R")
+source( helperPath )
+
 sizesCollection <- collectSizes(paste0(mantaAndPacBioDir, "/mantaExactCleanDeletionSizes.txt"), 
                                 paste0(mantaAndPacBioDir, "/mantaExactCleanInsertionSizes.txt"),
                                 paste0(mantaAndPacBioDir, "/mantaExactCleanTandupSizes.txt"),