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Create default StudyInfo.csv

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This commit is contained in:
Bryan Roessler
2024-07-31 20:38:28 -04:00
parent bab81f5461
commit 1374f4031d
1 changed files with 23 additions and 8 deletions
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31
workflow/qhtcp-workflow
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@@ -411,19 +411,36 @@ init_project() {
[[ -d $PROJECT_SCANS_DIR ]] || (mkdir -p "$PROJECT_SCANS_DIR" || return 1) [[ -d $PROJECT_SCANS_DIR ]] || (mkdir -p "$PROJECT_SCANS_DIR" || return 1)
# Create the study info file
if [[ ! -f $STUDY_INFO_FILE ]]; then
echo "Create a default study info file?";
if ask "You can edit this file in the qhtcp module"; then
cat <<-EOF > "$STUDY_INFO_FILE"
"ExpNumb","ExpLabel","BackgroundSD","ZscoreJoinSD","AnalysisBy"
EOF
fi
fi
# Write skeleton files in csv # Write skeleton files in csv
# If we have to convert to xlsx later, so be it # If we have to convert to xlsx later, so be it
cat <<-EOF > "$DRUG_MEDIA_FILE" echo "In the future we will copy the DrugMedia file from robot here"
# cat <<-EOF > "$DRUG_MEDIA_FILE"
EOF # EOF
cat <<-EOF > "$MASTER_PLATE_FILE"
# TODO here we'll copy scans from robot but for now let's pause and wait for transfer
echo "In the future we will copy the MasterPlate file from robot here"
# cat <<-EOF > "$MASTER_PLATE_FILE"
EOF # EOF
# TODO here we'll copy scans from robot but for now let's pause and wait for transfer # TODO here we'll copy scans from robot but for now let's pause and wait for transfer
echo "In the future we will copy scans from robot here" echo "In the future we will copy scans from robot here"
@@ -611,7 +628,7 @@ easy() {
done done
# Copy templates # Copy templates
rsync -a "$EASY_DIR"/{figs,Ptmats} "$EASY_RESULTS_DIR" rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
# Launch matlab # Launch matlab
# matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script" # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
@@ -706,8 +723,6 @@ module qhtcp
qhtcp() { qhtcp() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
if [[ -d $QHTCP_PROJECT_DIR ]]; then if [[ -d $QHTCP_PROJECT_DIR ]]; then
echo "A project already exists at $QHTCP_PROJECT_DIR" echo "A project already exists at $QHTCP_PROJECT_DIR"
ask "Safely update $QHTCP_PROJECT_DIR from the $QHTCP_TEMPLATE_DIR template?" ask "Safely update $QHTCP_PROJECT_DIR from the $QHTCP_TEMPLATE_DIR template?"
@@ -749,7 +764,7 @@ qhtcp() {
# Ask user to edit STUDY_INFO_FILE # Ask user to edit STUDY_INFO_FILE
if ! ((YES)) && ask "Would you like to edit $STUDY_INFO_FILE to add or modify studies?"; then if ! ((YES)) && ask "Would you like to edit $STUDY_INFO_FILE to add or modify studies?"; then
cat <<-EOF cat <<-EOF
Give each experiment the labels you wish to be used for the plots and specific files. Give each experiment labels to be used for the plots and specific files.
Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
Auto-entry suggestion: $next_study_entry Auto-entry suggestion: $next_study_entry