[galaxy, snpEff integration] was Re: I'm alive

Hi David.

Great to hear your keen to get going on galaxy integration - I'm hoping we'll have a v2.9 release ready to go in the next 4 weeks, but I wouldn't expect Galaxy connectivity to be fully ready by then.. since I'm sure it will take some serious field testing!

As to approach. The REST interface would be my preferred route, but Blend4j (https://github.com/jmchilton/blend4j) looks like it could also fit the bill. Does it use the same API ? The way to start is to list the functionality needed and see which one offers them all. There's also some overlap here with the GenomeSpace project, too (i.e. providing save/load functionality to a Galaxy server as a virtual file system and supporting the Galaxy data/file type model for file I/O).

Re snpEff: I'm not 100% about direct integrating snpEff's GUI - I'd like to get some recommendations from others about how useful it would be. There certainly is a need to implement a mechanism for visualising outputs of variant analysis pipelines in a Jalview-like way, but it needs a bit of experimentation. It sounds perfect as a third-party module for OSGi - and yet another reason why we need to get the Jalview 3 alpha together!



On 02/02/2015 07:23, David Roldán Martínez wrote:

Hi Jim,

I'll take a look, sure! Do you want me to integrate blend4j (https://github.com/jmchilton/blend4j) with Jalview or do you prefer me to develop an integration module from scratch? I see Galaxy project has a REST API.

Please, forward me any training material you think it can be useful for me. I've learnt a lot but never is enough. :slight_smile:

As for SnpEff I wasn't meaning to implement a parser. There's no need to reinvent the wheel. As far as licences allos that, I was talking about integrating SnpEff/SnpSift VCF with Jalview. Something like an input data JPanel somewhere in Jalview with a button to be pressed and display graphically the results.

I'm starting Galaxy integration right now! :wink: As soon as I have taken a deeper look, I'll let you know when I expect it to be finished. When is the next Jalview release?


Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
The University of Dundee is registered Scottish charity: No.SC015096

Then, dear community, please let me know the desired functionalities and I’ll start asap. If you prefer using the REST interface directly, I’ll proceed that way.
As to SnpEff, I was not refering to use the same GUI. In fact, there’s no sense because SnpEff is command-line oriented while Jalview isn’t. I was thinking about managing the same input/output info. But let’s start with Galaxy and leave this discussion for later on.