Hi, On Thu, Nov 21, 2019 at 12:47:26AM +0100, Andreas Tille wrote: > 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.
I now renamed the package and the Git archive according to your suggestion to libbio-db-hts-perl[1] > > 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. Done. > > > 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 how to make sure libhts will be found? Kind regards Andreas. [1] https://salsa.debian.org/med-team/libbio-db-hts-perl -- http://fam-tille.de
