Re: All predependencies for qiime 1.9? [Was: Bug#793585: ITP: ea-utils -- command-line tools for processing biological sequencing data]
Hi Tim,
On Wed, Jul 29, 2015 at 03:24:39PM +0100, Tim Booth wrote:
> I've confirmed ea-utils builds fine on Trusty and switched to your
> improved package, thanks.
:-)
> So, QIIME...
>
> I've just packaged and tested an initial QIIME 1.9.1 on my local
> machine. This is a bugfix release on 1.9.0, as the version suggests,
> but I'm getting test failures relating to RDP-Classifier so I need to
> work out what has happened there and fix the issue.
OK, we are not yet there to upload to Debian due to the pre-dependencies
you are mentioning below.
> QIIME now relies on a thing called "burrito-fillings" and associated
> "burrito".
I upgraded your burrito package (please regard SVN!) and uploaded it to
the new queue. Burrito-fillings will follow.
> As far as I can see these are supposed to replace the
> troublesome Python-Cogent but they don't - you need both for QIIME
> 1.9.x! (Yes, there is obvious copy-paste code between the two).
I do not know what actual trouble your are refering to but I remember
that I tried to establish the test suite of python-cogent into the
Debian package and failed terribly. I stalled this effort and I only
remember that depending of removing some totally unrelated pieces of
code inside he test suite had totally unpredictable results for the
outcome of the test suite. I have never seen such strange things in any
other Python module. It seems there will be no change since there is no
release in the last three years. Do you have any more detailed
information?
> My current RDP test failure is to do with something in the latest
> burrito-fillings library.
Did you nticed that there is a new upstream version 0.1.1?
I need to wait until python-burrito is accepted and a quick look
uncovered another pre-dependency: python-skbio. I'll work down all your
work - please watch Debian Med SVN closely for any updates that might
help you.
> Furthermore, burrito needs the python-future library from here:
>
> https://github.com/PythonCharmers/python-future
I was perfectly able to run the test suite with Debian's own
python-future / python3-future.
> I've pushed the packaging for that to SVN (I still don't understand how
> the heck GIT is supposed to work on Alioth)
I'm fine with SVN as long as its in VCS. Git is explained in the Debian
Med policy - just have a look there and it should be easy. More specific
questions are welcome for sure.
> but it's not a biomedical
> library at all, just a generic compatibility layer, so maybe should not
> be under Deb Med. What do you think?
We have a lot of non-medical stuff here. If our team needs to maintain
a package for whatever reason it is good to have it under our control.
If another team wants to "steal" some work from us that would be
perfectly fine. :-)
> I'll let you know when I'm done with my debugging and push the Burrito
> stuff too.
Just checkout the latest python-burrito from SVN and latest upstream
from python-burrito-fillings. May be that might solve some problems.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: