debian/changelog

-virulencefinder (0.0+git20190402.4812325-1) UNRELEASED; urgency=medium
+virulencefinder (0.0+git20190402.4812325-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
-  TODO: https://pypi.org/project/cgecore/
+  * Initial release (Closes: #929497)
 
- -- Andreas Tille <tille@debian.org>  Fri, 24 May 2019 14:36:44 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 24 May 2019 22:05:35 +0200

debian/clean

+test/Hit_in_genome_seq.fsa
+test/Virulence_genes.fsa
+test/data.json
+test/results.txt
+test/tmp/out_virulence_ecoli.xml

debian/control

@@ -7,22 +7,39 @@ Build-Depends: debhelper (>= 12~),
                dh-python,
                python3,
                python3-tabulate,
-               python3-cgecore
+               python3-cgecore,
+               ncbi-blast+ <!nocheck>
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder
 Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git
 Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder
 
 Package: virulencefinder
-Architecture: any
+Architecture: all
 Depends: ${misc:Depends},
          ${python3:Depends},
          python3,
          python3-tabulate,
-         python3-cgecore
-Description: identify viruelnce genes in total or partial sequenced isolates of bacteria
+         python3-cgecore,
+         ncbi-blast+,
+         kma
+Description: identify virulence genes in total or partial sequenced isolates of bacteria
  The VirulenceFinder service contains one Python script
  virulencefinder.py which is the script of the latest version of the
  VirulenceFinder service. VirulenceFinder identifies viruelnce genes in
  total or partial sequenced isolates of bacteria - at the moment only E.
  coli, Enterococcus, S. aureus and Listeria are available.
+
+Package: virulencefinder-examples
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: virulencefinder
+Description: example data for virulencefinder
+ The VirulenceFinder service contains one Python script
+ virulencefinder.py which is the script of the latest version of the
+ VirulenceFinder service. VirulenceFinder identifies viruelnce genes in
+ total or partial sequenced isolates of bacteria - at the moment only E.
+ coli, Enterococcus, S. aureus and Listeria are available.
+ .
+ This package provides an example for virulencefinder including
+ ecoli database.

debian/rules

@@ -12,8 +12,8 @@ override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	./virulencefinder.py -i test/test.fsa -o test/ -p test/database/ -mp blastn -x -q ; \
 	file=test/results_tab.tsv ; \
-	DIFF=$$(diff $file test/test_results.tsv) ; \
-	if [ "$DIFF" == "" ] && [ -s $file ] ; then \
+	DIFF=$$(diff "$$file" test/test_results.tsv) ; \
+	if [ "$$DIFF" = "" ] && [ -s "$$file" ] ; then \
 	    echo "TEST SUCCEEDED" ; \
 	else \
 	   echo "TEST FAILED"; \

debian/tests/run-unit-test

 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=virulencefinder
 
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -14,5 +14,19 @@ fi
 cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
 
-#do_stuff_to_test_package#
+# upstream test script is a bit broken
+virulencefinder.py -i test.fsa -o . -p database -mp blastn -x -q
+file=results_tab.tsv
+if [ ! -s $file ] ; then
+   echo "Result file $file is missing."
+   echo "TEST FAILED"
+   exit 1
+fi
+DIFF=$(diff $file test_results.tsv)
+if [ "$DIFF" = "" ] ; then
+   echo "TEST SUCCEEDED"
+else
+   echo "TEST FAILED"
+fi

debian/virulencefinder-examples.install

+test/*	usr/share/doc/virulencefinder/examples