

set -ex



echo "PREFIX=$PREFIX   CONDA_PREFIX=$CONDA_PREFIX"
amr_report -help
amrfinder --help
amrfinder_update --help
fasta_check -help
fasta2parts -help
gff_check -help
dna_mutation -help
curl --silent \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected
amrfinder -u
amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia > test_both.got
diff test_both.expected test_both.got

exit 0
