Hi Carnë, On Wed, Nov 20, 2019 at 11:24:19PM +0000, Carnë Draug wrote: > > when beeing here at BioHackathon I had some discussion about packaging > > ensembl libs. I'm not really sure what might be a good package to start > > but I picked libensembl-bio-db-hts-perl[1]. You see that I prefixed the > > upstream name by libensembl and postfixed by -perl as per Perl modules > > policy. Feel free to comment on that naming scheme. > > This is not a BioPerl package/distribution. While it is on the Bio:: > namespace, it is not authored or maintained by the BioPerl project.
Yes. That's that's why I had the (may be questionable) idea to use the ensembl prefix to make this clear. > BioPerl is not the only authority on the Bio:: namespace. OK. > About the package name, policy states that the package name should > match the main module name. In this case, the main module is > Bio::DB::HTS so the package should be named libbio-db-hts-perl. OK, fine for me to drop ensembl again. > > Unfortunately I was not able to tell the configure step where to find > > htslib. I'd assume it should be detected automatically but since it > > is not I tried the following three methods - all with no success: > > [...] > > 6. pkg-config (extra directories can be set in PKG_CONFIG_PATH > > environment variable) > > 7. common library locations: /usr /usr/local, /usr/share, /opt/local > > > > If none of the above succeeds but htslib is registered with pkg-config, the > > script > > will try using pkg-config paths (via ExtUtils::PkgConfig) without checking > > if header > > and library files exist. > > > > > > Any hint how to fix this? > > I have never used or installed this distribution. However, looking at > d/control the libextutils-pkgconfig-perl package does not appear on > build-depends. This seems to be required to find htslib automatically > (with pkg-config). > > That's my guess. Hmmm, $ git diff diff --git a/debian/control b/debian/control index e3d3a7a..794e917 100644 --- a/debian/control +++ b/debian/control @@ -6,6 +6,7 @@ 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, does not change anything. :-( Any other ideas? Thanks for your input anyway, Andreas. -- http://fam-tille.de
