[Debian-med-packaging] Qiime building.

[Andreas Tille]

On Tue, Aug 14, 2012 at 06:24:40PM +0100, Tim Booth wrote:
> 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.

Is Qiime actually that picky about versions?
 
> matplotlib is not quite the right version (wontfix)
> ParsInsert is missing (*)

You mean this one: http://sourceforge.net/projects/parsinsert/ ?

> R is 2.14 not 2.12 (wontfix)
> blast is 2.2.25 not 2.2.22 (wontfix)
> clearcut is missing (*)

URL???

> cluster_jobs_fp not set up (you need to do this for your cluster)
> mothur is missing (rebuilding it just now)

You mean just for your PPA right?

> numpy is not 1.5.1 (won't fix)
> pplacer is missing (*)

Found a publication: http://www.biomedcentral.com/1471-2105/11/538/
Download URL ?

> python is 2.7.3 not 2.7.2 (won't fix)
> raxmlHPC is missing

We do have just plain raxml.  Should we in addition package a HPC version?

> rtax is missing (*)

URL???

> uclust is missing (needs manual install due to non-free-ness)

Any volunteer to nag the authors?

> usearch is missing (I thought there was a package for this somewhere ??)

This name does not ring a bell.  When seeking it seems to be mentioned
always in connection with uclust.
 
> * = 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.

I'd be very glad to guide you (or anybody else) into this.

Kind regards

        Andreas.

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