CSV2IVIS.txt

#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --job-name=processCmds

# Set file paths
DATAIVIS=/scratch/groups/jzeitzer/UKBB/Data/IVIS
DATACSV=/scratch/groups/jzeitzer/UKBB/Data/Outputs/timeSeries
DATACOMM=/scratch/groups/jzeitzer/UKBB/Data/Commands
CODEUKBB=/scratch/groups/jzeitzer/UKBB/Code/ukbb

# Export environment variables
export DATAIVIS
export DATACSV
export DATACOMM
export CODEUKBB

# Make sure directories exist
mkdir -p $DATAIVIS
mkdir -p $DATACSV
mkdir -p $DATACOMM

# Load modules
ml python/3.6 #.1
ml py-numpy/1.18.1_py36
ml py-scipy/1.4.1_py36
ml py-scikit-learn/0.24.2_py36
ml py-pandas/1.0.3_py36
ml R
wget http://cran.us.r-project.org
R CMD INSTALL nparACT_0.8.tar.gz

# Generate input files 
cd $DATACOMM
python3 /scratch/groups/jzeitzer/UKBB/Code/ukbb/chunkCSV.py

cd $CODEUKBB
for FILE in $DATACOMM/inputcsv_*.txt; do
    echo ${FILE}
    export FILE
    sbatch -n 1 -t 1-00:00:00 --job-name=CSV2IVIS --wrap="bash /scratch/groups/jzeitzer/UKBB/Code/ukbb/runIVIS.txt"
done