debian/control

@@ -15,7 +15,9 @@ Package: resfinder
 Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends},
-         bioperl,
+         resfinder-db,
+         python3-cgecore,
+         python3-tabulate,
          ncbi-blast+-legacy
 Description: identifies acquired antimicrobial resistance genes
  ResFinder identifies acquired antimicrobial resistance genes in total or

debian/rules

 #!/usr/bin/make -f
 
 %:
-	dh $@
-
-override_dh_auto_build:
-override_dh_auto_install:
-	echo "Upstream install target just fetches BioPerl which is now installed via Depends"
+	dh $@ --with python3

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=resfinder
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+
+resfinder.py -i test.fsa -o . -p /usr/share/resfinder/db -d aminoglycoside -t 0.90 -l 0.60