Andreas Tille pushed to branch master at Debian Med / virulencefinder
Commits: 02f97eb4 by Andreas Tille at 2019-05-24T13:07:47Z Citation information - - - - - df3b87fe by Andreas Tille at 2019-05-24T13:36:42Z More sophisticated packaging (not finished yet) - - - - - 7 changed files: - debian/control - + debian/docs - + debian/install - + debian/links - + debian/lintian-overrides - debian/rules - + debian/upstream/metadata Changes: ===================================== debian/control ===================================== @@ -3,7 +3,10 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 12~) +Build-Depends: debhelper (>= 12~), + dh-python, + python3, + python3-tabulate Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git @@ -11,10 +14,12 @@ Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder Package: virulencefinder Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends} +Depends: ${misc:Depends}, + ${python:Depends}, + python3, + python3-tabulate Description: identify viruelnce genes in total or partial sequenced isolates of bacteria - The VirulenceFinder service contains one python script + 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. ===================================== debian/docs ===================================== @@ -0,0 +1 @@ +README* ===================================== debian/install ===================================== @@ -0,0 +1 @@ +*.py usr/share/virulencefinder ===================================== debian/links ===================================== @@ -0,0 +1 @@ +usr/share/virulencefinder/virulencefinder.py usr/bin/virulencefinder.py ===================================== debian/lintian-overrides ===================================== @@ -0,0 +1,2 @@ +# see https://lists.debian.org/debian-med/2018/06/msg00043.html +virulencefinder: script-with-language-extension usr/bin/*.* ===================================== debian/rules ===================================== @@ -1,31 +1,21 @@ #!/usr/bin/make -f # DH_VERBOSE := 1 -export LC_ALL=C.UTF-8 -include /usr/share/dpkg/default.mk -# this provides: -# DEB_SOURCE: the source package name -# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision) -# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision -# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch -# DEB_VERSION_UPSTREAM: the package's upstream version -# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog -# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as -# specified by <https://reproducible-builds.org/specs/source-date-epoch/> - -# for hardening you might like to uncomment this: -# export DEB_BUILD_MAINT_OPTIONS=hardening=+all +export PYBUILD_SYSTEM=custom +export PYBUILD_CLEAN_ARGS=rm -rf test/results_tab.tsv %: - dh $@ + dh $@ --with python3 --buildsystem=pybuild -### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected -#override_dh_auto_test: +override_dh_auto_test: #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) -# do_stuff_for_testing + ./virulencefinder.py -i test/test.fsa -o test/ -mp blastn -x -q ; \ + file=test/results_tab.tsv ; \ + DIFF=$$(diff $file test/test_results.tsv) ; \ + if [ "$DIFF" == "" ] && [ -s $file ] ; then \ + echo "TEST SUCCEEDED" ; \ + else \ + echo "TEST FAILED"; \ + fi #endif - -### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script -#get-orig-source: -# . debian/get-orig-source ===================================== debian/upstream/metadata ===================================== @@ -0,0 +1,12 @@ +Reference: + Author: Katrine Grimstrup Joensen and Flemming Scheutz and Ole Lund and Henrik Hasman and Rolf S. Kaas and Eva M. Nielsen and Frank M. Aarestrup + Title: Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli + Journal: Journal of Clinical Microbiology + Year: 2014 + Volume: 52 + Number: 5 + Pages: 1501-10 + DOI: 10.1128/JCM.03617-13 + PMID: 24574290 + URL: https://jcm.asm.org/content/52/5/1501 + eprint: https://jcm.asm.org/content/jcm/52/5/1501.full-text.pdf View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/3fdcbf5e78c9c627e7a07ce740917a225bd1fa54...df3b87fefe9eb394eb4c2a48de3f963818b04136 -- View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/3fdcbf5e78c9c627e7a07ce740917a225bd1fa54...df3b87fefe9eb394eb4c2a48de3f963818b04136 You're receiving this email because of your account on salsa.debian.org.
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