#!/bin/sh 
source $HOME/.bashrc

module load cpu/0.15.4  
module load gcc/10.2.0
module load openjdk/11.0.2

#include the whole path for the output file
cmdline="perl /expanse/projects/ngbt/opt/expanse/fastml/3.11/www/fastml/FastML_Wrapper.pl --MSA_file infile --outDir `pwd`/test $*"
echo $cmdline
$cmdline 

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"