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Re: How to submit software for addition to BioLinux?

Hi all,

I guess I have a ³simple² question but it might be a bit of a showstopper
- Bpipe relies on a number of java libraries that are fetched in binary
form from online repositories at build time. If I understand Debian policy
correctly, that is not allowable. I checked through the packages and a
number of them seem to be either unavailable in Debian or they are
available but not with recent enough versions.

If I understand the situation right, my options would be -

 - somehow get all these third party libraries submitted / updated into

 - package the source for all these libraries inside the Bpipe package and
have the package build all the dependent libraries it needs as part of its
own build. 

The first I am afraid would be far beyond the time I have to commit. The
second is probably also quite a lot of work, but its more feasible.

Are these my only options?

NB: this seems to be a similar situation to OpenClinica a few years ago.
Thread here:


Cheers / thanks!


On 6/02/2015 7:51 am, "Andreas Tille" <andreas@an3as.eu> wrote:

>Hi Simon,
>I'm writing you as a member of the Debian Med team.
>On Thu, Feb 05, 2015 at 06:08:49PM +0000, Tim Booth wrote:
>> It's great to hear that you are using Bio-Linux and want to contribute
>> your Bpipe package.  We also have a need for an effective lightweight
>> pipeline system that supports clusters and doesn't rely on a web client
>> (Galaxy) or a mountain of Java dependencies and remote services
>> (Taverna).
>> What we can do do is to submit the package to Debian Med
>> (https://wiki.debian.org/DebianMed) which is what I do with all my new
>> packages where possible.  Putting the package into Debian makes it
>> appear in Debian, Ubuntu, Mint and of course Bio-Linux so it's a big
>> win.
>> To have a Debian package one needs first to make the initial package and
>> then to maintain it as new versions come out or bugs are reported.  The
>> first bit is hard for you but easy for us.  The second bit is where you
>> can make it much easier for us by being the primary maintainer in Debian
>> and handling necessary updates.  (Don't worry that you are using
>> Bio-Linux rather than an Debian system - for Java apps it makes no
>> difference.)
>> To this end I've copied this to the Debian Med list.  Someone on the
>> list might fancy picking up the package - if not I'll have a look at it
>> myself but it will be a couple of weeks before I have time as I'm rushed
>> on various other jobs.  Either way, we'll take you through the initial
>> packaging then make sure you are set up to be the primary maintainer.
>> It's a bit of learning for you but you won't have to swallow the entire
>> 106 page Debian packagers' policy manual ;-)  Does that sound an OK
>> plan?
>I could also offer to help you getting started in a so called Mentoring
>of the Month project:
>    https://wiki.debian.org/DebianMed/MoM
>In short we would be really happy if you could help you to get the
>software you need into Debian and its derivatives.
>Kind regards
>       Andreas.
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