[Debian-med-packaging] Andreas pimping Ensembl packages

[William Spooner]

On 7 Dec 2011, at 13:52, Andreas Tille wrote:

> On Wed, Dec 07, 2011 at 12:36:08PM +0000, William Spooner wrote:
>> I won't go into the politics, but the Ensembl web application requires the old version of libwww-perl, and changing this is not trivial. Perl will allow an application to set a particular library path, hence selectively use a particular library version. Can this be engineered into the Debian packaging as an interim measure? 
> 
> Well, it somehow needs to be done.  But this is not a clean solution at
> all and will bidn ensembl to sticl in experimental as it is now.
> However, it makes testing an awfull pain because it needs to setup a
> dedicated chroot (to not kill your real installation).

It's a pain, I know, but I'm confident it can be addressed.

> 
> Is there any chance to file a bug report against ensembl upstream
> somehow.  Even if it is not trivial it should be done somehow sooner or
> later because not doing so will strike back at some point in time.  This
> question is totally independant from Debian packaging or not (and it's
> not political but rather technical).

Ensembl are aware of the issue, and will fix in due course, unless we (Eagle) fix it first and Ensembl accept the patch. Sadly it is not a trivial fix; can we blame libwww-perl for breaking their interface between releases?


> 
> I would really love if somebody would answer questions like this
> publicly on the mailinglist because (as I said previousely) this
> information is hidden from other helpers.  So please give me a signal
> what can be forewarded the thread at

>   http://lists.alioth.debian.org/pipermail/debian-med-packaging/2011-December/012720.html
> 
> and what not.  I would like to keep a record in the mailing list which
> somehow says: libwww-perl5.808 is needed for the time beeing.  It would
> be great to add a link to the ensembl bug tracker (I can perfectly open
> a ticket if needed if you give me a hint how to do this).

I will raise a ticket with Ensembl helpdesk that can perhaps be used for this purpose.

Best,

Will

--
William Spooner
william.spooner at eaglegenomics.com
http://www.eaglegenomics.com