python3_docker

#!/usr/bin/bash
source gdc-import.config.sh

# Usage: python3_docker script.py [ARGS]
# Run script.py in a python3 environment with json and requests packages

START_DOCKER="bash WUDocker/start_docker.sh"

# based on: https://www.freecodecamp.org/news/building-python-data-science-container-using-docker/
IMAGE="faizanbashir/python-datascience:3.6"

PY_SRC=$1
# Get absolute path of script
PY=$(readlink -f $PY_SRC)
PYTHON3="/usr/bin/python3"

shift
CMD_PY="$PYTHON3 $PY $@"

# Be able to read mapped dirs from command line
#MAPPED_DIR=". /home/m.wyczalkowski/Projects/GDAN/GDAN.catalog"
MAPPED_DIR=". /home/m.wyczalkowski/Projects/GDAN/GDAN.catalog $CATALOGD /storage1/fs1/dinglab/Active/Projects/CPTAC3/Common/CPTAC3.catalog"

#ARGS="-l"
# -l - send output to stdout
ARGS="-q dinglab -r"
CMD="$START_DOCKER -M compute1 -I $IMAGE $ARGS -c \"$CMD_PY\" $MAPPED_DIR"
#CMD="$START_DOCKER -M compute1 -I $IMAGE $MAPPED_DIR"
>&2 echo Running: $CMD
eval $CMD

#bash docker/WUDocker/start_docker.sh -I mwyczalkowski/python3_gdc:20230315 -c "/usr/local/bin/python3 /diskmnt/Projects/cptac_scratch/CPTAC3.workflow/discover/dev/20230314.REST-test/test1.py" -l .