Re: More bioperl modules need packaging
On Wed, 20 Nov 2019 at 17:51, Andreas Tille <andreas@an3as.eu> 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
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