Raoul J.P. Bonnal

@seandavi ok great. If you have time to give me some hints on how to start hacking the code I can try to implement it by myself and later on...

Correct but maybe other people are using an older version of the software. We could tag it as deprecated, do you like this idea?

What performing a demultiplexing without Illumina CASAVA ?

I like the idea, we must define a small set of specifications. I have a ready to go version in a Dev branch which uses rails style commands and let...

For what ? Please give us examples

Ok, I have a duty for the week end

SciRuby has no prefix so solving this could close #46

https://github.com/helios/bioruby-ngs/commit/9a45afb169ec7e1ddc726f0ee46ac59493994ea8

Trimmomatic can not handle concatenated gzip files. It is not a trimmomatic fault but it comes from Java, the bug still active http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4691425 but there is a workaround

can be related to https://github.com/rubygems/rubygems/issues/404 We are considering to switch to bundler but first we want to fix critical issues and later move on