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Fix perl modules

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This commit is contained in:
Bryan Roessler
2024-08-03 23:21:15 -04:00
parent 0149ade881
commit 95da97e7fc
1 changed files with 7 additions and 4 deletions
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workflow/qhtcp-workflow
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@@ -380,6 +380,7 @@ interactive_header() {
echo "$line" >> ~/.bashrc echo "$line" >> ~/.bashrc
fi fi
fi fi
declare -gx R_LIBS_USER="$HOME/R/$SCRIPT_NAME"
else else
debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME" debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME"
fi fi
@@ -584,14 +585,14 @@ install_dependencies() {
# Install R packages # Install R packages
for d in "${depends_r[@]}"; do for d in "${depends_r[@]}"; do
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}\"" debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\" repos=\"https://cloud.r-project.org\")}\""
"$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}" "$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\" repos=\"https://cloud.r-project.org\")}"
done done
# Install Bioc packages # Install Bioc packages
for d in "${depends_bioc[@]}"; do for d in "${depends_bioc[@]}"; do
debug "$RSCRIPT -e \"BiocManager::install(\"$d\")\"" debug "$RSCRIPT -e \"BiocManager::install(\"$d\", lib=\"$R_LIBS_USER\")\""
"$RSCRIPT" -e "BiocManager::install(\"$d\")" "$RSCRIPT" -e "BiocManager::install(\"$d\", lib=\"$R_LIBS_USER\")"
done done
hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules" hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
@@ -678,6 +679,7 @@ module easy
# * Don't create output in the scans folder, put it in an output directory # * Don't create output in the scans folder, put it in an output directory
# * The !!Results output files need standardized naming # * The !!Results output files need standardized naming
# * The input MasterPlate and DrugMedia sheets need to be converted to something standard like csv/tsv # * The input MasterPlate and DrugMedia sheets need to be converted to something standard like csv/tsv
# * This would allow them to be created programmatically as well
# #
# NOTES # NOTES
# #
@@ -2066,6 +2068,7 @@ main() {
declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp" declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv" declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy" declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy"
declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
if ((DEBUG)); then if ((DEBUG)); then
declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \ declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
PROJECTS PROJECT_NAME \ PROJECTS PROJECT_NAME \