Nilesh Patra pushed to branch master at Debian Med / hts-nim-tools
Commits: fb59dd26 by Nilesh Patra at 2020-11-08T03:06:38+05:30 Add manpage and corresponding build-depends to generate one - - - - - b7c50dcb by Nilesh Patra at 2020-11-08T03:25:47+05:30 Add preliminary autopkgtest - - - - - f4c0e9a0 by Nilesh Patra at 2020-11-08T03:27:28+05:30 Enhance metadata - - - - - 756283ec by Nilesh Patra at 2020-11-08T03:30:50+05:30 Add override - - - - - 7 changed files: - debian/control - + debian/lintian-overrides - + debian/manpages - debian/rules - + debian/tests/control - + debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/control ===================================== @@ -11,7 +11,9 @@ Build-Depends: debhelper-compat (= 13), nim-unicodeplus-dev, nim-regex-dev, nim-kexpr-dev, - nim-lapper-dev + nim-lapper-dev, + help2man, + libhts-dev Standards-Version: 4.5.0 Homepage: https://github.com/brentp/hts-nim-tools Vcs-Browser: https://salsa.debian.org/med-team/hts-nim-tools ===================================== debian/lintian-overrides ===================================== @@ -0,0 +1,2 @@ +# Looks like a false positive - the whatis entry is: "hts-nim-tools - manual page for hts-nim-tools" which sounds more or less, sensible +hts-nim-tools: useless-whatis-entry usr/share/man/man1/hts-nim-tools.1.gz ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/rules ===================================== @@ -12,6 +12,7 @@ override_dh_auto_build: #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim nim c --debuginfo:on --nimcache:$(NIMCACHE) --out:bin/hts-nim-tools -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim + help2man --no-info --no-discard-stderr --help-option="-h" ./bin/hts-nim-tools > debian/hts-nim-tools.1 override_dh_dwz: echo "I: not executing dwz, which fails because of Unknown DWARF DW_OP_0" @@ -20,4 +21,3 @@ override_dh_auto_clean: rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads src/copy_number_sampler rm -rf $(NIMCACHE) rm -rf bin - ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, nim-hts-examples (>= 0.3.12+ds-4), libhts-dev +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,19 @@ +#!/bin/bash +set -e + +pkg="hts-nim-tools" + +if [ "$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/nim-hts-examples/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP +gunzip -r * + +echo "Test 1" +hts-nim-tools bam-filter "tag_NM == 2 && tag_RG == 'SRR741410' && is_proper_pair" HG02002.bam | tail -5 +echo "=======================================" +echo "PASS" ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,10 @@ +--- +Archive: GitHub +Bug-Database: https://github.com/brentp/hts-nim-tools/issues +Bug-Submit: https://github.com/brentp/hts-nim-tools/issues/new +Changelog: https://github.com/brentp/hts-nim-tools/tags +Repository: https://github.com/brentp/hts-nim-tools.git +Repository-Browse: https://github.com/brentp/hts-nim-tools Registry: - Name: bio.tools Entry: NA View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/compare/b9f81a0cd792c907e29015a7448453ea56354f5a...756283eca886fe99d2068980bfa3a150fa28e434 -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/compare/b9f81a0cd792c907e29015a7448453ea56354f5a...756283eca886fe99d2068980bfa3a150fa28e434 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit