[Debian-med-packaging] Qiime building.

Tue Aug 14 17:24:40 UTC 2012

Hi Michael,

I'm still waiting for a few things to build but I've basically gathered
all the Qiime essentials, built for Precise, in the new Bio-Linux PPA:

https://launchpad.net/~nebc/+archive/bio-linux/+packages

On my test machine the result of "qiime print_qiime_config" is now:

System information
==================
         Platform:	linux2
   Python version:	2.7.3 (default, Aug  1 2012, 05:14:39)  [GCC 4.6.3]
Python executable:	/usr/bin/python

Dependency versions
===================
                     PyCogent version:	1.5.1
                        NumPy version:	1.6.1
                   matplotlib version:	1.1.1rc
                  biom-format version:	1.0.0c
                QIIME library version:	1.5.0
                 QIIME script version:	1.5.0
        PyNAST version (if installed):	1.1
RDP Classifier version (if installed):	rdp_classifier.jar

QIIME config values
===================
                     blastmat_dir:	/usr/share/ncbi/data
                    jobs_to_start:	1
pynast_template_alignment_blastdb:	None
                qiime_scripts_dir:	/usr/lib/qiime/bin/
   template_alignment_lanemask_fp:	None
                      working_dir:	.
     pynast_template_alignment_fp:	None
                    python_exe_fp:	python
                         temp_dir:	/tmp
                      blastall_fp:	blastall
                 seconds_to_sleep:	60
                  cluster_jobs_fp:	None

As for the self-tests, I get 13 failures but not all of these actually need to be fixed.
In general, if Qiime doesn't work with, say, the standard R version, the preferred fix
would be to patch Qiime rather than to bundle the legacy R if at all possible.
Also, the latest version of Qiime has added several new tools which are not yet packaged.

matplotlib is not quite the right version (wontfix)
ParsInsert is missing (*)
R is 2.14 not 2.12 (wontfix)
blast is 2.2.25 not 2.2.22 (wontfix)
clearcut is missing (*)
cluster_jobs_fp not set up (you need to do this for your cluster)
mothur is missing (rebuilding it just now)
numpy is not 1.5.1 (won't fix)
pplacer is missing (*)
python is 2.7.3 not 2.7.2 (won't fix)
raxmlHPC is missing
rtax is missing (*)
uclust is missing (needs manual install due to non-free-ness)
usearch is missing (I thought there was a package for this somewhere ??)

* = ParsInsert is a new dependency.  Could be a packaging job if you
fancy having a crack at it?  Same may be true of clearcut, pplacer,
rtax, and raxmlHPC.

Cheers,

TIM

> Thank you for the heads up. Does Qiime now pass its own self-tests out
> of the box on Debian unstable?
> 
> > If you have further questions feel free to ask.
> 
> Certainly
> 
> > Kind regards and thanks for your interest in Debian Med
> 
> You are very welcome; 'tis my pleasure to contribute.
> 
> >       Andreas.
> >
> > On Fri, Aug 10, 2012 at 08:57:59AM +0200, Steffen Möller wrote:
> >> Hi Michael,
> >>
> >> thank you for the introduction to your interest. I am CCing a few folks
> >> from Debian Med. Tim has some fame for his preparation of BioLinux.  And
> >> he is our man for qiime, seconded by Charles, if I got this right.
> >> Please sync with them. The new packages of yours would be great to see
> >> co-maintained on the Debian Med svn/git repository. For that you'd need
> >> an account on alioth.debian.org, which we then add to the Debian Med
> >> alioth project.
> >>
> >> Many greetings
> >>
> >> Steffen
> >>
> >> On 08/10/2012 12:04 AM, Michael Crusoe wrote:
> >> > Hello Steffan,
> >> >
> >> > I was going to submit a patch for building v2.0.4 of tophat on Ubuntu
> >> > but it looks like that was already fixed in the packaging repository
> >> > (though not pushed to Debian unstable yet).
> >> >
> >> > I did have to rebuild arb for Ubuntu. I'd be happy to write a recipe
> >> > to build arb for the DebianMed PPA.
> >> >
> >> > Other software I may package at a later date:
> >> >
> >> > jModelTest http://molecularevolution.org/software/phylogenetics/jmodeltest
> >> > dambe (under wine *shudder) http://dambe.bio.uottawa.ca/dambe.asp
> >> > AMOS http://sourceforge.net/apps/mediawiki/amos/index.php?title=Debian_installation
> >> > Darkhorse (after I get it to work from scratch) http://darkhorse.ucsd.edu/
> >> > mauve http://gel.ahabs.wisc.edu/mauve/
> >> >
> >> > I would like to help with the quality of the Qiime package as we
> >> > weren't able to make it match the capabilities of installing it via
> >> > the app-deploy script
> >> >
> >> > On Thu, Aug 9, 2012 at 2:34 PM, Steffen Möller <steffen_moeller at gmx.de> wrote:
> >> >> Hi Michael,
> >> >>
> >> >> I just saw your request to be added to the DebianMed PPA. What packages are you after?
> >> >>
> >> >> Cheers,
> >> >>
> >> >> Steffen
> >>
> >>
> >
> > --
> > http://fam-tille.de

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705
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