bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Beginning debug/cleanup

Browse Source
This commit is contained in:
Bryan Roessler
2024-07-29 11:17:21 -04:00
parent e734dcd93a
commit 1e92e97110
1 changed files with 11 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

18
workflow/qhtcp-workflow
View File

@@ -229,14 +229,19 @@ err() { echo "Error: $*" >&2; }
ask_pn() { ask_pn() {
unset PROJECT unset PROJECT
declare -g PROJECT declare -g PROJECT
example_pn="${PROJECT_PREFIX}_$(random_words 3)"
cat <<-EOF cat <<-EOF
Enter a new or existing project name, ex. ${PROJECT_PREFIX}_$(random_words 3) Enter a new or existing project name
If entering a new project, use the suggested prefix: ${PROJECT_PREFIX}_ If entering a new project, use the suggested prefix: ${PROJECT_PREFIX}_
You may choose any combination of words/characters following the prefix, but be sensible. You may choose any combination of words/characters following the prefix, but be sensible.
Make it descriptive and avoid spaces and special characters. Make it descriptive and avoid spaces and special characters.
Example: ${example_pn}
EOF EOF
read -r -p "Enter a new or existing project name: " PROJECT read -r -p "Enter a new or existing project name ($example_pn): " PROJECT
[[ -z $PROJECT ]] if [[ -z $PROJECT ]]; then
echo "Setting project name to the default: $example_pn"
PROJECT="$example_pn"
fi
} }
debug() { (( DEBUG )) && echo "Debug: $*"; } debug() { (( DEBUG )) && echo "Debug: $*"; }
# Not super portable but nice to have # Not super portable but nice to have
@@ -691,7 +696,6 @@ qhtcp() {
STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt" STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT" QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
APPS_DIR="$QHTCP_PROJECT_DIR/apps" APPS_DIR="$QHTCP_PROJECT_DIR/apps"
CODE_DIR="$QHTCP_PROJECT_DIR/Code" # legacy location, keeping until can port each script to APPS
STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv" STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
if [[ -d $QHTCP_PROJECT_DIR ]]; then if [[ -d $QHTCP_PROJECT_DIR ]]; then
@@ -1089,7 +1093,7 @@ r_gta_heatmaps() {
EOF EOF
script="$CODE_DIR/TSHeatmaps5dev2.R" script="$APPS_DIR/r/TSHeatmaps5dev2.R"
[[ -d $5 ]] || mkdir -p "$5" [[ -d $5 ]] || mkdir -p "$5"
@@ -1468,9 +1472,9 @@ main() {
SCANS_DIR="$d" SCANS_DIR="$d"
fi fi
done done
echo "Scans directory: $SCANS_DIR" echo "Using scans directory: $SCANS_DIR"
echo "Change the SCANS environment variable to override" echo "Change the SCANS environment variable to override"
echo "Example: SCANS=/path/to/other/scans ./qhtcp-workflow.sh" echo "Example: SCANS=/path/to/scans ./qhtcp-workflow"
# Set the automatic project directory prefix # Set the automatic project directory prefix
PROJECT_USER="$(whoami)" PROJECT_USER="$(whoami)"