Re: More bioperl modules need packaging
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 <tille@debian.org>
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
Reply to: