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

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

Hi Martin,

responses below


On Fri, Jul 4, 2014 at 9:50 AM, Martin MOKREJŠ <mmo...@gm...> wrote:

>
>
> Brian Haas wrote:
> > 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.
>
> Sure, take your time. Also, the packaging is an issue due to many
> different LICENSEs used in all the bundled tools. Just split it all into
> sub-packages, that's the only way.
>
>
Right...  that's definitely a cause for concern, which is why we keep the
third-party code isolated wherever possible, and should have a note in
there somewhere to follow the different licenses for the plugins.  We only
leverage code that has very lenient licensing, as we do for our code.



> So where does trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
> come from? It doesn't seem to be from
> http://www.genome.umd.edu/jellyfish.html or
> ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
>
>
It should have come from the jellyfish website.   In the upcoming Trinity
release, we're just going to bundle in the .tar.gz files for the code, and
have the makefile do the unpack/build as part of the Trinity build.  This
will go for RSEM-2.15 as well.

One of the key issues here is that there are some versions of the tools
where the usage has changed significantly (both the latest rsem and
jellyfish), so that our new version of Trinity will only be readily
compatible with those specific versions - which is why they get bundled in,
and Trinity will look in the plugins area to find what it needs.

After we get the next Trinity, Trinotate, and PASA releases out, we'll
rethink our bundling strategy.

best,

~b


> Martin
>
>
> >
> > cheers,
> >
> > ~brian
> >
> >
> > On Fri, Jul 4, 2014 at 8:46 AM, Martin MOKREJŠ <mmo...@gm...
> <mailto: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