David Miguel Susano Pinto pushed to branch master at Debian Med / libensembl-bio-db-hts
Commits: 8835cdb8 by David Miguel Susano Pinto at 2019-11-21T14:59:10Z Fix find of htslib, change upstream links, and other small fixes. * d/rules: fix finding htslib by not attempting to manually specify its location and leaving pkg-config to do its job. * d/compat: add file and set to 11 because my system is too old. * d/control: this fits better in the science section than perl; set debhelper to 11 because my build system is too old; add the libextutils-cbuilder-perl build dependency; use metacpan as the upstream location. * d/copyright: upstream releases to metacpan. * d/libbio-db-hts-perl.lintian-overrides: silence lintian about this package not being in the perl section. * d/upstream/metadata: remove empty sections and fill what I know about. * d/watch: releases to CPAN will appear on metacpan not github so watch metacpan for new releases not github. - - - - - 7 changed files: - + debian/compat - debian/control - debian/copyright - + debian/libbio-db-hts-perl.lintian-overrides - debian/rules - debian/upstream/metadata - debian/watch Changes: ===================================== debian/compat ===================================== @@ -0,0 +1 @@ +11 ===================================== debian/control ===================================== @@ -1,26 +1,24 @@ Source: libbio-db-hts-perl -Section: perl +Section: science Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Andreas Tille <[email protected]> -Testsuite: autopkgtest-pkg-perl -Build-Depends: debhelper-compat (= 12), - libmodule-build-perl, - libextutils-pkgconfig-perl, - libhts-dev -Build-Depends-Indep: perl, - libbio-perl-perl, - pkg-config +Build-Depends: debhelper (>= 11), + libbio-perl-perl, + libextutils-cbuilder-perl, + libextutils-pkgconfig-perl, + libhts-dev, + libmodule-build-perl, + perl Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git -Homepage: https://github.com/Ensembl/Bio-DB-HTS +Homepage: https://metacpan.org/release/Bio-DB-HTS +Testsuite: autopkgtest-pkg-perl Package: libbio-db-hts-perl Architecture: any -Depends: ${perl:Depends}, - ${shlibs:Depends}, - ${misc:Depends} +Depends: ${perl:Depends}, ${misc:Depends} Description: Perl interface to the HTS library HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call @@ -29,7 +27,7 @@ Description: Perl interface to the HTS library compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension - ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the + 'csi' (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package provides a Perl interface to the HTS library. ===================================== debian/copyright ===================================== @@ -1,6 +1,6 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: https://metacpan.org/release/Bio-DB-HTS Upstream-Name: Bio-DB-HTS -Source: https://github.com/Ensembl/Bio-DB-HTS Files: * Copyright: 2015-2019 EMBL-European Bioinformatics Institute ===================================== debian/libbio-db-hts-perl.lintian-overrides ===================================== @@ -0,0 +1,3 @@ +## Even though this is a perl library, its use cases are so specific +## that science is a better fit. +libbio-db-hts-perl: wrong-section-according-to-package-name libbio-db-hts-perl => perl ===================================== debian/rules ===================================== @@ -1,11 +1,4 @@ #!/usr/bin/make -f -# DH_VERBOSE := 1 - %: dh $@ - -override_dh_auto_configure: - # dh_auto_configure -- --prefix=/usr - # dh_auto_configure -- --htslib-includedir=/usr/include - HTSLIB_DIR=/usr/include dh_auto_configure ===================================== debian/upstream/metadata ===================================== @@ -1,12 +1,6 @@ -Reference: - Author: - Title: - Journal: - Year: - Volume: - Number: - Pages: - DOI: - PMID: - URL: - eprint: +--- +Archive: CPAN +Bug-Database: https://github.com/Ensembl/Bio-DB-HTS/issues +Name: Bio-DB-HTS +Repository: https://github.com/Ensembl/Bio-DB-HTS.git +Repository-Browse: https://github.com/Ensembl/Bio-DB-HTS ===================================== debian/watch ===================================== @@ -1,4 +1,3 @@ -version=4 - -opts="mode=git,pretty=98+git%cd.%h" \ - https://github.com/Ensembl/Bio-DB-HTS.git HEAD +version=3 +https://metacpan.org/release/Bio-DB-HTS \ + .*/Bio-DB-HTS-v?(\d[\d.-]*)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/commit/8835cdb8c66fadc5ca141767d093761fc1919c44 -- View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/commit/8835cdb8c66fadc5ca141767d093761fc1919c44 You're receiving this email because of your account on salsa.debian.org.
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