From 36fe4278c42c276a5d5ef6b5e5876feb05b6e67b Mon Sep 17 00:00:00 2001 From: Zhiyu <zhiyu.zhao@utsouthwestern.edu> Date: Wed, 13 Nov 2024 10:29:06 -0600 Subject: [PATCH] 11132024 --- V2.2/oda_analysis.sh | 4 +++- V2.2/run_analysis.sh | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/V2.2/oda_analysis.sh b/V2.2/oda_analysis.sh index 34bb1eb..89ee62d 100755 --- a/V2.2/oda_analysis.sh +++ b/V2.2/oda_analysis.sh @@ -34,10 +34,12 @@ then else echo "CAUTION: Output folder is NOT deleted. New analysis result will be saved in the existing folder. Result files will be overwritten if they have the same names with the previous ones." fi +else + mkdir -p $OUTPUT_FOLDER fi if [ "$QUEUE" == "local" ] then - sh $ODA_DIR/run_analysis.sh $ODA_DIR $INPUT_FILE $OUTPUT_FOLDER + sh $ODA_DIR/run_analysis.sh $ODA_DIR $INPUT_FILE $OUTPUT_FOLDER 2>&1 | tee -a "$OUTPUT_FOLDER/ODA_run"$(date +%s"."%N)".log" else sbatch -p $QUEUE $ODA_DIR/run_analysis.sh $ODA_DIR $INPUT_FILE $OUTPUT_FOLDER fi diff --git a/V2.2/run_analysis.sh b/V2.2/run_analysis.sh index 3ec1a27..37fc50e 100644 --- a/V2.2/run_analysis.sh +++ b/V2.2/run_analysis.sh @@ -5,5 +5,5 @@ ODA_MODULE=$ODA_DIR/r_with_packages_4.3.2.sif #Link to: /archive/CRI/shared/Sing INPUT_FILE=$2 OUTPUT_FOLDER=$3 echo $ODA_MODULE -singularity exec $ODA_MODULE Rscript /ODA/ODA.R $INPUT_FILE $OUTPUT_FOLDER 2>&1 | tee -a "$OUTPUT_FOLDER/ODA_run"$(date +%s"."%N)".log" +singularity exec $ODA_MODULE Rscript /ODA/ODA.R $INPUT_FILE $OUTPUT_FOLDER -- GitLab