#!/bin/sh
# This is for running on COMET
#test change 

source $HOME/.bashrc

echo "CIPRES_THREADSPP=$CIPRES_THREADSPP"
echo "CIPRES_NP=$CIPRES_NP"
echo "running:"

module reset
module load gcc/10.2.0
module load python/3.8.5
module load spades/3.15.2 

export MODULEPATH=/expanse/projects/ngbt/opt/expanse/modules:$MODULEPATH
module load meta-marc


cmdline="$*"
echo $cmdline
$cmdline

module load openjdk/11.0.2
for f in *; do
    if [[ -d $f ]]; then
        jar cvf ${f}.zip $f
        echo "archived subdir $f as ${f}.zip"
    fi
done
echo "... moving on"