[Bio-linux-dev] Qiime update

[Mike Cox]

Hi Tim,

PyNAST is now behaving and running for me, (I've just checked by running
core_qiime_analyses.py, so anything not run by this I can't comment on).  I
am getting an error message that Matplotlib is an untested version when it
hits the beta diversity section, specifically when calculating the PCoAs,
but the resulting PCoAs seem to look OK, so it doesn't look like the
version in actual use has broken things.

Thanks!

Mike

On Thu, Nov 3, 2011 at 18:08, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi All,
>
> Following on from the previous discussion, I have uploaded a new qiime
> and bio-linux-qiime package, along with a fix to chimeraslayer.  This
> should address the issues that Mike reported and also clear up some but
> not all of the problems reported by "qiime print_qiime_config -t".
> Specifically I now get:
>
> FastTree is in path and version is supported ... ok
> INFERNAL is in path and version is supported ... ok
> AmpliconNoise install looks sane. ... ok
> blast is in path and version is supported ... FAIL
> blastall_fp is set to a valid path ... ok
> blastmat_dir is set to a valid path. ... ok
> cdbtools is in path and version is supported ... ok
> cd-hit is in path and version is supported ... ok
> no obvious problems with ChimeraSlayer install ... ok
> clearcut is in path and version is supported ... FAIL
> cluster_jobs_fp is set to a valid path and is executable ... ok
> denoiser aligner is ready to use ... ok
> local qiime_config has no extra params ... ok
> maptplotlib version is supported ... FAIL
> mothur is in path and version is supported ... ERROR
> muscle is in path and version is supported ... FAIL
> numpy version is supported ... ok
> pynast version is supported ... ok
> pynast_template_alignment_blastdb, if set, is set to a valid path ... ok
> pynast_template_alignment, if set, is set to a valid path ... ok
> python_exe_fp is set to a working python env ... ok
> python is in path and version is supported ... ok
> qiime_scripts_dir, if set, is set to a valid path ... ok
> raxmlHPC is in path and version is supported ... FAIL
> temp_dir, if set, is set to a valid path ... ok
> template_alignment_lanemask, if set, is set to a valid path ... ok
> uclust is in path and version is supported ... ok
> working_dir, if set, is set to a valid path ... ok
>
> If you are still seeing other failures, please check you have upgraded
> the packages:
>
> % dpkg -s qiime bio-linux-qiime chimeraslayer | grep ^Version
> Version: 1.3.0-0ubuntu6
> Version: 1:1.3.0bl-6
> Version: 20101212-1ubuntu5
>
> If there are still issues after checking this then let me know.
>
> Of the remaining issues, a couple more things I should be able to fix,
> but some of the others seem to be due to us having newer versions,
> rather than older versions, of dependencies, and I'm not going to make a
> downgraded package unless someone tells me it really is needed (ie. a
> real error, not just a test warning).
>
> Cheers,
>
> TIM
>
> --
> 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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