[Bio-linux-dev] Qiime update

[Tim Booth]

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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