Re: status of trinityrnaseq 2015/05/21

[Andreas Tille <andreas@an3as.eu>]

Hi Michael,

On Thu, May 21, 2015 at 10:44:56PM +0000, Michael Crusoe wrote:
> Jeff (jab@debian.org) recently emailed about the status of the packages of
> the Trinity RNASeq assembler and I thought I'd update the group while I was
> at it.
>
> trinityrnaseq package: waiting on libjung-java, rsem, express,
> transdecoder, and jaligner. Otherwise all the tests run successfully for me.

I'd love to provide good news about new queue processing but I have no
idea why it is currently that slow. :-(
 
> libjung-java package: need to split into two source package: one free and
> one contrib.

If I read this correctly you see a chance that we can depend from the free
part?

> This has the pleasant side effect of making the patches that
> migrate the code off of the obsolete collections15 framework much clearer.
> Will also test out newly free'd libcolt-free package
> https://lists.debian.org/debian-med/2015/03/msg00150.html

+1
 
> rsem: waiting for r-bioc-ebseq; needs manpages
> 
> r-bioc-ebseq: waiting for r-cran-blockmodeling
> 
> r-cran-blockmodeling: in NEW queue
> https://ftp-master.debian.org/new/r-cran-blockmodeling_0.1.8-1.html

We could try pinging ftpmaster ranking those packages that are at the
end of a chain of dependency higher in their priority list.

> express: In NEW queue https://ftp-master.debian.org/new/express_1.5.1-1.html
> could benefit from having binary installed to another location and
> symlinked to /usr/bin/express
> 
> transdecoder: in NEW queue
> https://ftp-master.debian.org/new/transdecoder_2.0.1+dfsg-1.html
> 
> jaligner: in NEW queue:
> https://ftp-master.debian.org/new/jaligner_1.0-1.html

Thanks a lot for this overview

     Andreas.

-- 
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