diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow index 4bceb509..87160196 100755 --- a/workflow/qhtcp-workflow +++ b/workflow/qhtcp-workflow @@ -569,6 +569,7 @@ easy() { 'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder. EOF + EASY_DIR="$APPS_DIR/matlab/easy" script="$EASY_DIR/EASYConsole.m" # Copy templates @@ -703,7 +704,8 @@ qhtcp() { OUT_DIR="/mnt/data/out/qhtcp" STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt" QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT" - APPS_DIR="$QHTCP_PROJECT_DIR/apps" + QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp" + STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp" STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv" if [[ -d $QHTCP_PROJECT_DIR ]]; then @@ -781,7 +783,7 @@ qhtcp() { # TODO eventually we could run this on multiple results dirs simultaneously with some refactoring if ((YES)) || [[ ${#EASY_RESULTS_DIRS[@]} -eq 1 ]]; then # In automatic mode just choose the first OUT DIR in the list - EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose + EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose the frist one else echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR" echo "Here is a list: " @@ -1468,9 +1470,7 @@ main() { # Global directory variables TEMPLATES_DIR="$SCRIPT_DIR/templates" - QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp" - STUDY_TEMPLATE_DIR="$QHTCP_TEMPLATE_DIR/ExpTemplate" - EASY_DIR="$SCRIPT_DIR/apps/matlab/easy" + APPS_DIR="$SCRIPT_DIR/apps" DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match SCANS="${SCANS:-"./scans":-"/mnt/data/ExpJobs"}" SCANS_HEIRARCHY=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs") # search for an existing scans dir in this order