Hi Lance, Björn, Dan

We are several scientists working on metagenomics in France and at a previous 
GUGGO  (western France User Group) meeting, we mention the fact to "benchmark" 
our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and 
the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy 
Solution) pipeline using Swarm. We already have had some exchanges with Björn 
concerning metagenomics flavours on Docker, and I think it will be particularly 
interesting to exchange one with each other. The Qiime integration was started 
in march by colleagues from Brest Ifremer centre. I was just trying to install 
and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on 
the list, I can contact them.

All the best,

Yvan 

----- Mail original -----
> De: "Björn Grüning" <bjoern.gruen...@gmail.com>
> À: "Lance Parsons" <lpars...@princeton.edu>, "Daniel Blankenberg" 
> <d...@bx.psu.edu>
> Cc: "Galaxy Dev List" <galaxy-dev@lists.galaxyproject.org>
> Envoyé: Mercredi 7 Octobre 2015 14:25:38
> Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP,  call for collaborators)
> 
> Hi Lance,
> 
> I will help if I can. I also think we should begin too write 2-3 nice
> tools in the beginning to test the handshake between them and lay the
> ground work. This will also help to get familiar with the tool.
> 
> I still hope some one else from the community shows interest! :)
> 
> Thanks,
> Bjoern
> 
> Am 06.10.2015 um 20:33 schrieb Lance Parsons:
> > I agree that it would be very nice to get the data flowing between each
> > of the tools and to be able to mix/match with other tools. That is an
> > area of Galaxy tool-dev that I'm less familiar with, so any help would
> > be greatly appreciated.
> > 
> > As for the manual massaging, I agree, however, at this point I'm really
> > hoping that the changes between Qiime versions are manageable, esp. once
> > we have the data types and basic framework of the tools down.
> > 
> > Along that front, I would very much like to get something usable (at
> > least for some specific workflows) done sooner rather than later, then
> > be able to iterate, adding new tools, datatypes, etc. as we move
> > forward. Does that sound reasonable? I love the idea of a Metagenomics
> > toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One
> > thing I would like to do soon then, would be to define some
> > functionality for the first round. What would be very helpful would be
> > if you, Bjoern, etc. could help make sure the first round lays the
> > proper groundwork so I/we don't have to redo things for later
> > iterations, but we can build on a solid foundation.
> > 
> > Thanks so much for the input, help, etc. It is very much appreciated.
> > 
> > - Lance
> > 
> >> Daniel Blankenberg <mailto:d...@bx.psu.edu>
> >> October 6, 2015 at 10:21 AM
> >> Hi Lance,
> >>
> >> I looked at this a bit ago and had similar concerns, particularly with
> >> the outputs and inputs not being well-defined. In addition to the
> >> output tar ball —> local, extract —> upload not being great, as you
> >> mention, the input datatypes, etc, could use some work — in the very
> >> least, we should definitely create a nice biom datatype and have some
> >> converters available (import and export).
> >>
> >> Definitely worth spending some extra time to make sure that we have
> >> the data flowing well between each of the different parts/tools, and
> >> even better to make sure that its done in a way that allows mixing and
> >> matching with other non-qiime tools.
> >>
> >>
> >> One thing that we want to avoid is large amounts of manual massaging
> >> of the automatically generated xml; fixing things up once might not be
> >> too bad, but having to do it with each new tool version can be
> >> “frustrating". Although perhaps having a good starting point and only
> >> needing to manually modify for any updates could be good enough (I’m
> >> not very familiar with the extent of typical changes between qiime
> >> versions to make a call on how much changes).
> >>
> >>
> >>
> >>
> >> Dan
> >>
> >> (resending since I received a message bounce from list)
> >>
> >>
> >>
> >> Daniel Blankenberg <mailto:d...@bx.psu.edu>
> >> October 6, 2015 at 9:59 AM
> >> Hi Lance,
> >>
> >> I looked at this a bit ago and had similar concerns, particularly with
> >> the outputs and inputs not being well-defined. In addition to the
> >> output tar ball —> local, extract —> upload not being great, as you
> >> mention, the input datatypes, etc, could use some work — in the very
> >> least, we should definitely create a nice biom datatype and have some
> >> converters available (import and export).
> >>
> >> Definitely worth spending some extra time to make sure that we have
> >> the data flowing well between each of the different parts/tools, and
> >> even better to make sure that its done in a way that allows mixing and
> >> matching with other non-qiime tools.
> >>
> >>
> >> One thing that we want to avoid is large amounts of manual massaging
> >> of the automatically generated xml; fixing things up once might not be
> >> too bad, but having to do it with each new tool version can be
> >> “frustrating". Although perhaps having a good starting point and only
> >> needing to manually modify for any updates could be good enough (I’m
> >> not very familiar with the extent of typical changes between qiime
> >> versions to make a call on how much changes).
> >>
> >>
> >>
> >>
> >> Dan
> >>
> >>
> >>
> >> Lance Parsons <mailto:lpars...@princeton.edu>
> >> October 5, 2015 at 5:26 PM
> >> I was recently asked if I could provide a QIIME analysis pipeline for
> >> 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
> >>
> >> I did a bit of looking around for existing Galaxy wrappers and found
> >> an application that generates the wrappers for QIIME scripts for
> >> Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well
> >> written application that does a great job of wrapping the QIIME
> >> scripts for Galaxy. However, there are a few things about it that
> >> don't quite fit my needs.
> >>
> >> 1. The tools output tgz files of all of the output files. This means
> >> that to execute a pipeline, the user would have to download the tgz
> >> files, untar, and then upload whichever file(s) are needed for the
> >> next step.
> >> 2. There is no toolshed repository to install the dependencies for
> >> these tools, making it a tricky for administrators to automate and
> >> also maintain various versions of QIIME going forward.
> >> 3. There are no toolshed versions of the tools themselves, which also
> >> makes installation and integration a bit tricky and makes it hard to
> >> me to create and manage updates, fixes, tweaks, etc. There are also no
> >> tests, etc.
> >>
> >> For these reasons I decided to investigate the feasibility of using
> >> the generated wrappers as a basis for a "toolshed" version of QIIME.
> >> If anyone is interested in helping, or has suggestions, or is working
> >> on something related, I'd be very happy to collaborate.
> >>
> >> The repository for the WIP is at
> >> https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0.
> >> There is also a package on the testtoolshed as well as a first pass at
> >> package_qiime_1_9_1
> >> (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1_9_1).
> >>
> >>
> > 
> > 
> > 
> > ___________________________________________________________
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> ___________________________________________________________
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-- 
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
Yvan Le Bras, PhD @Yvan2935 <°))))>< 
e-Biogenouest project http://www.e-biogenouest.org 
CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex 
tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 
yvan.le_b...@irisa.fr 
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