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 > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ -- Tim Booth <[email protected]> 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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
