How to submit software for addition to BioLinux?
Hi Simon,
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?
Cheers,
TIM
> Hello,
>
> We are big users of BioLinux here at MCRI so firstly I would like to
> say thank you for this wonderful contribution to the bioinformatics
> community.
>
> I am the author of a tool called Bpipe which is a command line tool
> for building and running bioinformatics pipelines. I was wondering
> what your criteria are for inclusion and whether you would consider
> including Bpipe into BioLinux? Bpipe has been published in
> Bioinformatcs<http://bioinformatics.oxfordjournals.org/content/28/11/1525> and is getting quite popular. It would be really nice to have it included in BioLinux and I would be very happy to help with any work involved. Bpipe only requires Java to work and is completely stand alone so it is very easy to add.
>
> Many thanks,
>
> Simon Sadedin
> Murdoch Childrens Research Institute
> Bioinformatics
>
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--
Tim Booth <tbooth@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://environmentalomics.org/bio-linux
+44 1491 69 2297
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