On Wed, 20 Nov 2019 at 17:51, Andreas Tille <[email protected]> wrote: > > Hi Carnë, > > 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. BioPerl is not the only authority on the Bio:: namespace. 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. > 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. ~ carandraug
