Re: [Transdecoder-users] Announcement: Transdecoder release r20140704

[Brian H. <bh...@br...>]

Thanks, Martin.  I've CC'd the trinity-developers list.  We'll take all
your comments into consideration.  It'll be some time before it all meets
your expectations (if that's even an option for us).  For now, our (perhaps
my) goals have been quite simple: keep everything self-contained and
minimize dependencies.  I entirely agree about that evil wget (which is one
of the reasons why I put the 'make simple' in there).  This version will be
incorporated as a plugin in the upcoming Trinity, along with Jellyfish-2
(even if currently to your dismay), and Trinity will do the 'make simple'
to avoid pulling down pfam via wget.

cheers,

~brian


On Fri, Jul 4, 2014 at 8:46 AM, Martin MOKREJŠ <mmo...@gm...> wrote:

> Brian Haas wrote:
> > Greetings all,
> >
> > The latest release of TransDecoder is now available:
> >
> >
> http://sourceforge.net/projects/transdecoder/files/TransDecoder_r20140704.tar.gz/download
> >
> > including minor changes from the previous release to ensure better
> compatibility with other projects, including Trinity, PASA, and Trinotate
> >
> > Release notes:
> >
> > -added 'make simple' to build just the essential components involving
> parafly and cdhit
> >
> > -removed the 'cds.' prefix from the pep and cds sequence accessions.
>
>
> Hi Brian,
>   I just tested the new and have some comments:
>
> 1. In the past the files were tar.bz2 instead of tar.gz as of now. It
> helps distro maintainers if the URLs and filenames remain stable. It is
> also a common habit that if one unpacks MyApp-2.4c.tar.gz that it extracts
> into MyApp-2.4c/ subdirectory. Although it seems your today's archive file
> complies with this I think trinity does not and not sure how long will it
> last. ;)
>
> 2. It is evil that the "make compile" step runs wget to download 1.4GB
> large PFAM file. Please put it under different "target" in your Makefile's.
> Not only, I already have the files on my system and I certainly do not want
> to waste my bandwidth.
>
> 3. I would like to add this to Gentoo Linux but that won't ever be allowed
> if the package is huge glue of other tools. For example, I have already
> cd-hit installed and installing TransDecoder would try to overwrite
> existing files, and will be denied. If you would like to get the package
> accepted into Linux distros and save developers time resolving the knotted
> layout, please introduce some configure- or Makefile-based checks and bail
> out if they are not installed. You can keep the crazy layout/setup as an
> alternative for users who think this is the right way to go (while it is
> not).
>
> 4. I wanted to post trinityrnaseq-users list about this but ... it is
> confusing that trinity and transdecoders place overlapping 3rd-party stuff
> under its own source tree. The
> http://trinityrnaseq.sourceforge.net/#installation page it totally quiet
> how all there hidden obstackles. I recommend you to sum up a simple listing
> of required/optional tools, their versions and URLs. If possible, drop them
> from the TransDecoder_r20140704/3rd_party and also from the plugins
> subdirectory somewhere under trinity*.
>
> 5. In the current setup, both transdecoder, trinity are un-manageable for
> a Linux distro. One cannot force some version dependencies, the tools
> download what they want to on their own instead of just running a compiler
> ... and tehy overwrite other applications files.
>
> 6. BTW, I realized quorum package looks for jellyfish-1.11 while on the
> web I found only jellyfish-2.x. Incidentally, I see jellyfish-1.11 under
> trinity*. Huh. Would you please tell me: whether trinity uses an "old"
> jellyfish version of teh same package? Or is that that incidentally same
> name? Why can't trinity use jellyfish-2.x installed already on the system.
>
> I wish it helps you and other devs to cleanup the interesting package,
> though I did not get to install it yet.
>
> Thank you,
> Martin
>



-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas