[med-svn] [Git][med-team/resfinder][master] 3 commits: Fix dependencies

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / resfinder


Commits:
4eaf3b49 by Andreas Tille at 2019-11-15T11:54:28Z
Fix dependencies

- - - - -
0340013a by Andreas Tille at 2019-11-15T11:54:38Z
Add autopkgtest

- - - - -
8f57c464 by Andreas Tille at 2019-11-15T12:02:23Z
Cleanup packaging

- - - - -


4 changed files:

- debian/control
- debian/rules
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
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
=====================================
@@ -1,8 +1,4 @@
 #!/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
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,18 @@
+#!/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



View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6...8f57c4646a7b3e59ec16a02f062430cec365a5e1

-- 
View it on GitLab: https://salsa.debian.org/med-team/resfinder/compare/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6...8f57c4646a7b3e59ec16a02f062430cec365a5e1
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