[med-svn] [Git][med-team/virulencefinder][master] 4 commits: Example package

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / virulencefinder


Commits:
8aca68cc by Andreas Tille at 2019-05-24T19:44:26Z
Example package

- - - - -
623afd24 by Andreas Tille at 2019-05-24T19:50:47Z
Fix tests

- - - - -
29715127 by Andreas Tille at 2019-05-24T20:01:27Z
Fix tests

- - - - -
ebfc5f0f by Andreas Tille at 2019-05-24T20:07:20Z
Depends: kma, Upload to unstable

- - - - -


9 changed files:

- debian/changelog
- + debian/clean
- debian/control
- debian/rules
- debian/tests/run-unit-test
- + debian/virulencefinder-examples.install
- debian/docs → debian/virulencefinder.docs
- debian/install → debian/virulencefinder.install
- debian/links → debian/virulencefinder.links


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
-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 at debian.org>  Fri, 24 May 2019 14:36:44 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 24 May 2019 22:05:35 +0200


=====================================
debian/clean
=====================================
@@ -0,0 +1,5 @@
+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
=====================================
@@ -1,7 +1,7 @@
 #!/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
=====================================
@@ -0,0 +1 @@
+test/*	usr/share/doc/virulencefinder/examples


=====================================
debian/docs → debian/virulencefinder.docs
=====================================


=====================================
debian/install → debian/virulencefinder.install
=====================================


=====================================
debian/links → debian/virulencefinder.links
=====================================



View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/0273a5da4ae6041e536fcfdf73c32674670b6d6a...ebfc5f0fb41e715ec2d1c56e33f3e36b6fa9cbff

-- 
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/0273a5da4ae6041e536fcfdf73c32674670b6d6a...ebfc5f0fb41e715ec2d1c56e33f3e36b6fa9cbff
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